Re: [gmx-users] help about ibi

[Mark Abraham]

Hi,

Something went wrong earlier in your workflow. Check your log files, etc.

Mark
On Nov 13, 2013 3:57 AM, "guozhicheng222"  wrote:

> Hi:
>
> When I am running the ibi procedure, I get the following error message:
>
>
>
>  A coordinate in file conf.gro does
> not contain a '.'
>
> Additionally, I check the coordinate file of confout.gro in step_001. It
> showed that 'nan' symbol appeared in confout.gro.
>
> What is wrong with this? How can I fix it? I am very appreciating for
> anyone's help.
>
> Best Wishes!
>
> Zhicheng Guo
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Re: [gmx-users] help about logfile

[Justin Lemkul]

On 11/11/13 5:04 AM, guozhicheng222 wrote:

Hi

I am confusing with the output file (.log) about the sample frequency
(frames) in my simulation. The average information in .log file is
'Statistics over 31 steps using 3001 frames' where nstxout =4000 and
nstlog =4000. While, 'Statistics over 31 steps using 20001 frames',
appeared in .log file, where nstxout =15 and nstlog =15. In my opinion, the
former sample frequency should be 75 frames rather than 3001 frames and the
latter is right. I want to know how can I control the sample frequency,
arbitrarily.



Check to make sure you set nstlog correctly in the first run.  Look for the 
value in the .log file itself.  It is highly unlikely that something so 
fundamental and simple is being executed incorrectly in one run, but correctly 
in another.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Help to simulate gas mixture

[Mark Abraham]

The principle is the same as at
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
On Nov 3, 2013 6:55 PM, "ali.nazari"  wrote:

> Dear Friends,
>
> I am just a beginner in using GROMCS-4.6.3 and I want to simulate gas
> mixture, the same as mixture of O2 and N2, any help(the same as introducing
> a reference, not GROMACS manual b/c there is no explanation about gas
> mixture) is appreciated.
>
> Kind Regards,
> Ali
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Help-to-simulate-gas-mixture-tp5012193.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Help on itp and pdb

[Justin Lemkul]

Please don't reply to the entire digest; the archive is hopelessly confused as 
it is, but let's not make it any worse ;)


On 9/6/13 2:29 PM, R R S Pissurlenkar wrote:

If I use the topology and coordinates of a small molecule from ATB for docking
(structure.pdb / structure.itp which match in atom numbering and sequence);
after docking and saving the structure_dock.pdb, the atom numbering does not
match the numbering in the structure.itp file.  This causes errors during
simulation.
How to regular the numbering so that it matches the structure.itp file from ATB


The numbering of the atoms in the coordinate file should have no relevance on 
the .itp file, which must be numbered from 1.  If atoms in the coordinate file 
are out of order with respect to the topology, there's no real choice but to 
reorder them manually in a text editor, but that's only something you should 
ever have to do once.


If you need more explicit advice, please provide exact input, output, and any 
relevant error messages (copied and pasted from the terminal, please).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] help

[Justin Lemkul]

On 9/4/13 6:04 AM, Prajisha Sujaya wrote:

  I am facing a problem while simulating the tRNA molecule
while converting pdb to gro,
Fatal error:
Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms
while sorting atoms.

force field used  3 (AMBER96 protein, nucleic AMBER94), water model TIP3P.
i checked in gromacs error list, in that they mentioned simply re-name the
atoms in your coordinate
file
,
how to rename the atom in coordinate file



Use a text editor.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Help with Error Message

[Tsjerk Wassenaar]

An editor is a program to edit the text in a file: gedit, nano, vi, emacs,
... It'll be the equivalent of Windows' Notepad. Can you find a tutor
around to help you out with the basic usage of Linux? It's always difficult
to plunge into several different things at the same time, here 'using
linux', 'performing simulations', and probably 'theory of molecular
dynamics'. It helps to take one topic at a time, but that is not always
possible.

Cheers,

T.




On Tue, Aug 27, 2013 at 10:56 PM, Rafael I. Silverman y de la Vega <
rsilv...@ucsc.edu> wrote:

> a text editor
>
>
> On Tue, Aug 27, 2013 at 1:54 PM, The One And Only  >wrote:
>
> > What kind of editor should I open it in? I have Pymol, but I don't know
> if
> > it's the right one.
> > --
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-- 
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Re: [gmx-users] Help with Error Message

[Rafael I. Silverman y de la Vega]

a text editor


On Tue, Aug 27, 2013 at 1:54 PM, The One And Only wrote:

> What kind of editor should I open it in? I have Pymol, but I don't know if
> it's the right one.
> --
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Re: [gmx-users] Help with Error Message

[The One And Only]

What kind of editor should I open it in? I have Pymol, but I don't know if
it's the right one.
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Re: [gmx-users] Help with Error Message

[Tsjerk Wassenaar]

Hi ...,

You should have had a look at the topology file format in an earlier step.
At the end is a listing of molecules. As it says in the tutorial, you
replaced solvent by ions, and you have to make changes in the topology file
to match that replacement. Open the file in an editor, have a look around,
try to see where the number of solvent molecules is listed, and make the
changes.

Cheers,

Tsjerk


On Tue, Aug 27, 2013 at 10:41 PM, The One And Only wrote:

> I've moved on from that point; now I'm stuck at where it asks me to remove
> molecules of solvent from the topology file.
>
>
> On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar 
> wrote:
>
> > Hey :)
> >
> > Sorry for replying a bit late. But the issues you mention in this and the
> > other posts are usually solved by closely reading the text of the
> tutorial,
> > not only the commands.
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > On Sun, Aug 25, 2013 at 3:44 AM, The One And Only  > >wrote:
> >
> > > Never mind, I'm dumb. I just realized that protein.pdb means i have to
> > > specify which protein i want like "1qlz.pdb" and not actually type
> > > "protein.pdb" BUT THANKS GUYS!!
> > >
> > >
> > > On Sat, Aug 24, 2013 at 6:40 PM, The One And Only <
> chappybo...@gmail.com
> > > >wrote:
> > >
> > > > so how do i solve the protein.pdb issue?
> > > >
> > > >
> > > > On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul 
> > wrote:
> > > >
> > > >>
> > > >>
> > > >> On 8/24/13 9:26 PM, The One And Only wrote:
> > > >>
> > > >>> that's something i know nothing about; I just graduated from high
> > > school
> > > >>> and I have no background or experience in open source projects or
> > > >>> programs
> > > >>> like pymol/gromacs. My professor wants me to be able to produce a
> > > setup,
> > > >>> simulation, and analysis within a week so I'm pretty desperate
> right
> > > now
> > > >>> in
> > > >>> terms of getting help. Do you know how to get the right .pdb file
> in
> > my
> > > >>> working directory?
> > > >>>
> > > >>>
> > > >> Rudimentary Unix commands like cp and mv are covered in any
> Unix/Linux
> > > >> tutorial.  Google can find lots of good ones.  Producing a quality
> > > >> simulation cannot be rushed, and if you don't know the fundamentals
> of
> > > >> navigating the command line and directory structure, it's nearly
> > > >> impossible.  You need to invest time in learning the environment
> > before
> > > >> doing anything, I'm afraid.  Just to give a bit of perspective, we
> > used
> > > to
> > > >> train our undergrads for nearly a full semester (at least 2-3
> months)
> > > >> before requiring them to do any "real" work.  At least a week or two
> > of
> > > >> that time was spent getting used to command line and Linux in
> general.
> > > >>
> > > >> -Justin
> > > >>
> > > >> --
> > > >> ==**
> > > >>
> > > >> Justin A. Lemkul, Ph.D.
> > > >> Postdoctoral Fellow
> > > >>
> > > >> Department of Pharmaceutical Sciences
> > > >> School of Pharmacy
> > > >> Health Sciences Facility II, Room 601
> > > >> University of Maryland, Baltimore
> > > >> 20 Penn St.
> > > >> Baltimore, MD 21201
> > > >>
> > > >> jalemkul@outerbanks.umaryland.**edu <
> > jalem...@outerbanks.umaryland.edu>|
> > > (410)
> > > >> 706-7441
> > > >>
> > > >> ==**
> > > >> --
> > > >> gmx-users mailing listgmx-users@gromacs.org
> > > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > > >> * Please search the archive at http://www.gromacs.org/**
> > > >> Support/Mailing_Lists/Search<
> > > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > > >> * Please don't post (un)subscribe requests to the list. Use the www
> > > >> interface or send it to gmx-users-requ...@gromacs.org.
> > > >> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> > > http://www.gromacs.org/Support/Mailing_Lists>
> > > >>
> > > >
> > > >
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
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> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> http://lists.g

Re: [gmx-users] Help with Error Message

[The One And Only]

I've moved on from that point; now I'm stuck at where it asks me to remove
molecules of solvent from the topology file.


On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar  wrote:

> Hey :)
>
> Sorry for replying a bit late. But the issues you mention in this and the
> other posts are usually solved by closely reading the text of the tutorial,
> not only the commands.
>
> Cheers,
>
> Tsjerk
>
>
> On Sun, Aug 25, 2013 at 3:44 AM, The One And Only  >wrote:
>
> > Never mind, I'm dumb. I just realized that protein.pdb means i have to
> > specify which protein i want like "1qlz.pdb" and not actually type
> > "protein.pdb" BUT THANKS GUYS!!
> >
> >
> > On Sat, Aug 24, 2013 at 6:40 PM, The One And Only  > >wrote:
> >
> > > so how do i solve the protein.pdb issue?
> > >
> > >
> > > On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul 
> wrote:
> > >
> > >>
> > >>
> > >> On 8/24/13 9:26 PM, The One And Only wrote:
> > >>
> > >>> that's something i know nothing about; I just graduated from high
> > school
> > >>> and I have no background or experience in open source projects or
> > >>> programs
> > >>> like pymol/gromacs. My professor wants me to be able to produce a
> > setup,
> > >>> simulation, and analysis within a week so I'm pretty desperate right
> > now
> > >>> in
> > >>> terms of getting help. Do you know how to get the right .pdb file in
> my
> > >>> working directory?
> > >>>
> > >>>
> > >> Rudimentary Unix commands like cp and mv are covered in any Unix/Linux
> > >> tutorial.  Google can find lots of good ones.  Producing a quality
> > >> simulation cannot be rushed, and if you don't know the fundamentals of
> > >> navigating the command line and directory structure, it's nearly
> > >> impossible.  You need to invest time in learning the environment
> before
> > >> doing anything, I'm afraid.  Just to give a bit of perspective, we
> used
> > to
> > >> train our undergrads for nearly a full semester (at least 2-3 months)
> > >> before requiring them to do any "real" work.  At least a week or two
> of
> > >> that time was spent getting used to command line and Linux in general.
> > >>
> > >> -Justin
> > >>
> > >> --
> > >> ==**
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Postdoctoral Fellow
> > >>
> > >> Department of Pharmaceutical Sciences
> > >> School of Pharmacy
> > >> Health Sciences Facility II, Room 601
> > >> University of Maryland, Baltimore
> > >> 20 Penn St.
> > >> Baltimore, MD 21201
> > >>
> > >> jalemkul@outerbanks.umaryland.**edu <
> jalem...@outerbanks.umaryland.edu>|
> > (410)
> > >> 706-7441
> > >>
> > >> ==**
> > >> --
> > >> gmx-users mailing listgmx-users@gromacs.org
> > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > >> * Please search the archive at http://www.gromacs.org/**
> > >> Support/Mailing_Lists/Search<
> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > >> * Please don't post (un)subscribe requests to the list. Use the www
> > >> interface or send it to gmx-users-requ...@gromacs.org.
> > >> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> > http://www.gromacs.org/Support/Mailing_Lists>
> > >>
> > >
> > >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Help with Error Message

[Tsjerk Wassenaar]

Hey :)

Sorry for replying a bit late. But the issues you mention in this and the
other posts are usually solved by closely reading the text of the tutorial,
not only the commands.

Cheers,

Tsjerk


On Sun, Aug 25, 2013 at 3:44 AM, The One And Only wrote:

> Never mind, I'm dumb. I just realized that protein.pdb means i have to
> specify which protein i want like "1qlz.pdb" and not actually type
> "protein.pdb" BUT THANKS GUYS!!
>
>
> On Sat, Aug 24, 2013 at 6:40 PM, The One And Only  >wrote:
>
> > so how do i solve the protein.pdb issue?
> >
> >
> > On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 8/24/13 9:26 PM, The One And Only wrote:
> >>
> >>> that's something i know nothing about; I just graduated from high
> school
> >>> and I have no background or experience in open source projects or
> >>> programs
> >>> like pymol/gromacs. My professor wants me to be able to produce a
> setup,
> >>> simulation, and analysis within a week so I'm pretty desperate right
> now
> >>> in
> >>> terms of getting help. Do you know how to get the right .pdb file in my
> >>> working directory?
> >>>
> >>>
> >> Rudimentary Unix commands like cp and mv are covered in any Unix/Linux
> >> tutorial.  Google can find lots of good ones.  Producing a quality
> >> simulation cannot be rushed, and if you don't know the fundamentals of
> >> navigating the command line and directory structure, it's nearly
> >> impossible.  You need to invest time in learning the environment before
> >> doing anything, I'm afraid.  Just to give a bit of perspective, we used
> to
> >> train our undergrads for nearly a full semester (at least 2-3 months)
> >> before requiring them to do any "real" work.  At least a week or two of
> >> that time was spent getting used to command line and Linux in general.
> >>
> >> -Justin
> >>
> >> --
> >> ==**
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 601
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul@outerbanks.umaryland.**edu |
> (410)
> >> 706-7441
> >>
> >> ==**
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >> * Please search the archive at http://www.gromacs.org/**
> >> Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> >> * Please don't post (un)subscribe requests to the list. Use the www
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> >>
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Re: [gmx-users] Help with Error Message

[The One And Only]

Never mind, I'm dumb. I just realized that protein.pdb means i have to
specify which protein i want like "1qlz.pdb" and not actually type
"protein.pdb" BUT THANKS GUYS!!


On Sat, Aug 24, 2013 at 6:40 PM, The One And Only wrote:

> so how do i solve the protein.pdb issue?
>
>
> On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 8/24/13 9:26 PM, The One And Only wrote:
>>
>>> that's something i know nothing about; I just graduated from high school
>>> and I have no background or experience in open source projects or
>>> programs
>>> like pymol/gromacs. My professor wants me to be able to produce a setup,
>>> simulation, and analysis within a week so I'm pretty desperate right now
>>> in
>>> terms of getting help. Do you know how to get the right .pdb file in my
>>> working directory?
>>>
>>>
>> Rudimentary Unix commands like cp and mv are covered in any Unix/Linux
>> tutorial.  Google can find lots of good ones.  Producing a quality
>> simulation cannot be rushed, and if you don't know the fundamentals of
>> navigating the command line and directory structure, it's nearly
>> impossible.  You need to invest time in learning the environment before
>> doing anything, I'm afraid.  Just to give a bit of perspective, we used to
>> train our undergrads for nearly a full semester (at least 2-3 months)
>> before requiring them to do any "real" work.  At least a week or two of
>> that time was spent getting used to command line and Linux in general.
>>
>> -Justin
>>
>> --
>> ==**
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul@outerbanks.umaryland.**edu | 
>> (410)
>> 706-7441
>>
>> ==**
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
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>> * Can't post? Read 
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>
>
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Re: [gmx-users] Help with Error Message

[The One And Only]

so how do i solve the protein.pdb issue?


On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul  wrote:

>
>
> On 8/24/13 9:26 PM, The One And Only wrote:
>
>> that's something i know nothing about; I just graduated from high school
>> and I have no background or experience in open source projects or programs
>> like pymol/gromacs. My professor wants me to be able to produce a setup,
>> simulation, and analysis within a week so I'm pretty desperate right now
>> in
>> terms of getting help. Do you know how to get the right .pdb file in my
>> working directory?
>>
>>
> Rudimentary Unix commands like cp and mv are covered in any Unix/Linux
> tutorial.  Google can find lots of good ones.  Producing a quality
> simulation cannot be rushed, and if you don't know the fundamentals of
> navigating the command line and directory structure, it's nearly
> impossible.  You need to invest time in learning the environment before
> doing anything, I'm afraid.  Just to give a bit of perspective, we used to
> train our undergrads for nearly a full semester (at least 2-3 months)
> before requiring them to do any "real" work.  At least a week or two of
> that time was spent getting used to command line and Linux in general.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
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> * Can't post? Read 
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Re: [gmx-users] Help with Error Message

[Justin Lemkul]

On 8/24/13 9:26 PM, The One And Only wrote:

that's something i know nothing about; I just graduated from high school
and I have no background or experience in open source projects or programs
like pymol/gromacs. My professor wants me to be able to produce a setup,
simulation, and analysis within a week so I'm pretty desperate right now in
terms of getting help. Do you know how to get the right .pdb file in my
working directory?



Rudimentary Unix commands like cp and mv are covered in any Unix/Linux tutorial. 
 Google can find lots of good ones.  Producing a quality simulation cannot be 
rushed, and if you don't know the fundamentals of navigating the command line 
and directory structure, it's nearly impossible.  You need to invest time in 
learning the environment before doing anything, I'm afraid.  Just to give a bit 
of perspective, we used to train our undergrads for nearly a full semester (at 
least 2-3 months) before requiring them to do any "real" work.  At least a week 
or two of that time was spent getting used to command line and Linux in general.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Help with Error Message

[The One And Only]

that's something i know nothing about; I just graduated from high school
and I have no background or experience in open source projects or programs
like pymol/gromacs. My professor wants me to be able to produce a setup,
simulation, and analysis within a week so I'm pretty desperate right now in
terms of getting help. Do you know how to get the right .pdb file in my
working directory?


On Sat, Aug 24, 2013 at 6:23 PM, Rafael I. Silverman y de la Vega <
rsilv...@ucsc.edu> wrote:

> It sounds like you dont have the .pdb file in your working directory.
> Perhaps you need to learn a bit about unix filesystems
>
>
> On Sat, Aug 24, 2013 at 6:18 PM, The One And Only  >wrote:
>
> > So I started following some tutorials online since I didn't get a
> response
> > last time. the tutorial I'm using is:
> > http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/
> > I followed that tutorial to the second page and got stuck at the step
> where
> > it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p
> protein.top
> > -ignh
> > I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for
> > the water model but got the following error message:
> > Opening force field file
> > /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b
> > Reading protein.pdb...
> >
> > ---
> > Program pdb2gmx, VERSION 4.6.3
> > Source code file:
> > /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593
> >
> > File input/output error:
> > protein.pdb
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > Help please?
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> >
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Re: [gmx-users] Help with Error Message

[Rafael I. Silverman y de la Vega]

It sounds like you dont have the .pdb file in your working directory.
Perhaps you need to learn a bit about unix filesystems


On Sat, Aug 24, 2013 at 6:18 PM, The One And Only wrote:

> So I started following some tutorials online since I didn't get a response
> last time. the tutorial I'm using is:
> http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/
> I followed that tutorial to the second page and got stuck at the step where
> it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p protein.top
> -ignh
> I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for
> the water model but got the following error message:
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b
> Reading protein.pdb...
>
> ---
> Program pdb2gmx, VERSION 4.6.3
> Source code file:
> /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593
>
> File input/output error:
> protein.pdb
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Help please?
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Help needed in installation

[Tsjerk Wassenaar]

Hi Sonika,

cmake needs a specification of the path where the source code is. In
addition to that, it is best to build it in a separate directory. As
explained on the website, in your gromacs directory:

mkdir build
cd build
cmake ../
make
make install

Hope it helps,

Tsjerk



On Tue, Jul 2, 2013 at 8:51 PM, Sonika Gahlawat
wrote:

> Hi everyone,
>
> I am trying to install Gromacs on OS X and following the installation
> guide, in section 4.1, I get an output shown as follows:
> Sonikas-MacBook-Pro:Downloads sonikagahlawat$ cd gromacs-4.6.2
> Sonikas-MacBook-Pro:gromacs-4.6.2 sonikagahlawat$ cmake
> cmake version 2.8.11.1
> Usage
>
>   cmake [options] 
>   cmake [options] 
>
> Options
>   -C   = Pre-load a script to populate the cache.
>   -D := = Create a cmake cache entry.
>   -U   = Remove matching entries from CMake cache.
>   -G  = Specify a makefile generator.
>   -T= Specify toolset name if supported by
> generator.
>   -Wno-dev= Suppress developer warnings.
>   -Wdev   = Enable developer warnings.
>   -E  = CMake command mode.
>   -i  = Run in wizard mode.
>   -L[A][H]= List non-advanced cached variables.
>   --build= Build a CMake-generated project binary
> tree.
>   -N  = View mode only.
>   -P= Process script mode.
>   --find-package  = Run in pkg-config like mode.
>   --graphviz=[file]   = Generate graphviz of dependencies.
>   --system-information [file] = Dump information about this system.
>   --debug-trycompile  = Do not delete the try_compile build tree.
> Only useful on one try_compile at a time.
>   --debug-output  = Put cmake in a debug mode.
>   --trace = Put cmake in trace mode.
>   --warn-uninitialized= Warn about uninitialized values.
>   --warn-unused-vars  = Warn about unused variables.
>   --no-warn-unused-cli= Don't warn about command line options.
>   --check-system-vars = Find problems with variable usage in system
> files.
>   --help-command cmd [file]   = Print help for a single command and exit.
>   --help-command-list [file]  = List available listfile commands and exit.
>   --help-commands [file]  = Print help for all commands and exit.
>   --help-compatcommands [file]= Print help for compatibility commands.
>   --help-module module [file] = Print help for a single module and exit.
>   --help-module-list [file]   = List available modules and exit.
>   --help-modules [file]   = Print help for all modules and exit.
>   --help-custom-modules [file]= Print help for all custom modules and exit.
>   --help-policy cmp [file]= Print help for a single policy and exit.
>   --help-policies [file]  = Print help for all policies and exit.
>   --help-property prop [file] = Print help for a single property and exit.
>   --help-property-list [file] = List available properties and exit.
>   --help-properties [file]= Print help for all properties and exit.
>   --help-variable var [file]  = Print help for a single variable and exit.
>   --help-variable-list [file] = List documented variables and exit.
>   --help-variables [file] = Print help for all variables and exit.
>   --copyright [file]  = Print the CMake copyright and exit.
>   --help,-help,-usage,-h,-H,/?= Print usage information and exit.
>   --help-full [file]  = Print full help and exit.
>   --help-html [file]  = Print full help in HTML format.
>   --help-man [file]   = Print full help as a UNIX man page and
> exit.
>   --version,-version,/V [file]= Show program name/version banner and exit.
>
> Generators
>
> The following generators are available on this platform:
>   Unix Makefiles  = Generates standard UNIX makefiles.
>   Ninja   = Generates build.ninja files (experimental).
>   Xcode   = Generate Xcode project files.
>   CodeBlocks - Ninja  = Generates CodeBlocks project files.
>   CodeBlocks - Unix Makefiles = Generates CodeBlocks project files.
>   Eclipse CDT4 - Ninja= Generates Eclipse CDT 4.0 project files.
>   Eclipse CDT4 - Unix Makefiles
>   = Generates Eclipse CDT 4.0 project files.
>   KDevelop3   = Generates KDevelop 3 project files.
>   KDevelop3 - Unix Makefiles  = Generates KDevelop 3 project files.
>   Sublime Text 2 - Ninja  = Generates Sublime Text 2 project files.
>   Sublime Text 2 - Unix Makefiles
>   = Generates Sublime Text 2 project files.
>
> Sonikas-MacBook-Pro:gromacs-4.6.2 sonikagahlawat$ ccmake
> ccmake version 2.8.11.1
> Usage
>
>   ccmake 
>   ccmake 
>
> Options
>   -C   = Pre-load a script to populate

Re: [gmx-users] Help with modified gmx_covar

[Mark Abraham]

You need to call the newly compiled code. Either install the new version
and source GMXRC appropriately, or use a full path to the new version in
the build tree.

Mark


On Wed, Jun 5, 2013 at 11:05 AM, rohitarora  wrote:

> Dear Gmx users,
>
> I need to ask you about a doubt I have regarding changing an analysis tool
> in Gromacs. More specifically g_covar. I found the modified source code for
> gmx_covar.c [ gmx_covar.c
>   ] and I
> would
> like to replace the current g_covar with modified one. I copied the source
> code in the src/tools directory and built g_covar
>
> cp gmx_covar.c ../softwares/gromacs4.5.6/src/tools
> make
> (or make g_covar)
>
> It runs fine, but when I run g_covar again, it gives me the old options.
> The
> new one should have more flags in addition to the old ones, like:
> -clog
> -xpmc (you can find them in source code)
>
> Does anyone know if I am missing something? If someone could briefly tell
> me
> the steps, I would really appreciate it.
>
> Best
> Rohit
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Help-with-modified-gmx-covar-tp5008825.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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RE: [gmx-users] help with g_hydorder and g_polystat

[Emmanuel, Alaina]

That's ok. Thank you for your help. In the meantime, I might see if g_h2order 
is a good substitute for g_hydorder.


Kind Regards,

Alaina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin Lemkul [jalem...@vt.edu]
Sent: 01 May 2013 22:58
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat

On 5/1/13 8:44 AM, Emmanuel, Alaina wrote:
>
> No, using a trajectory file with g_hydorder hasn't made any difference. The 
> error is still the same.
>
> When I use g_polystat, I use the following command:
>
> g_polystat_d -f file.xtc  -s file.tpr -n polymer_backbone.ndx  -p persist.xvg 
> -o polystat.xvg
>
> Note: Using "polymer_backbone.ndx" yields fewer polymers with nan issues, 
> than using the whole polymer structure in an index file.
>

The g_hydorder problem is a bug in the code and I have filed a bug report on
Redmine.  I have no insight into what's going on with g_polystat, sorry.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] help with g_hydorder and g_polystat

[Justin Lemkul]

On 5/1/13 8:44 AM, Emmanuel, Alaina wrote:


No, using a trajectory file with g_hydorder hasn't made any difference. The 
error is still the same.

When I use g_polystat, I use the following command:

g_polystat_d -f file.xtc  -s file.tpr -n polymer_backbone.ndx  -p persist.xvg 
-o polystat.xvg

Note: Using "polymer_backbone.ndx" yields fewer polymers with nan issues, than 
using the whole polymer structure in an index file.



The g_hydorder problem is a bug in the code and I have filed a bug report on 
Redmine.  I have no insight into what's going on with g_polystat, sorry.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] help with g_hydorder and g_polystat

[Emmanuel, Alaina]

No, using a trajectory file with g_hydorder hasn't made any difference. The 
error is still the same.

When I use g_polystat, I use the following command: 

g_polystat_d -f file.xtc  -s file.tpr -n polymer_backbone.ndx  -p persist.xvg 
-o polystat.xvg

Note: Using "polymer_backbone.ndx" yields fewer polymers with nan issues, than 
using the whole polymer structure in an index file. 

Kind Regards,

Alaina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin Lemkul [jalem...@vt.edu]
Sent: 01 May 2013 10:58
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat

On 4/30/13 9:00 PM, Emmanuel, Alaina wrote:
> Hello Justin,
>
> My mdp file shows that the pbc was set to xyz.
>

Instead of analyzing a coordinate file, does it work with a trajectory?
Regarding g_polystat and the nan's, what command are you issuing?

-Justin

>
> Kind Regards,
>
> Alaina
>
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of Justin Lemkul [jalem...@vt.edu]
> Sent: 30 April 2013 16:10
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] help with g_hydorder and g_polystat
>
> On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:
>> Dear All,
>>
>> I'm fairly new to gromacs and having a bit of problem with the g_hydorder 
>> and g_polystat. Thanks in advanced for your time.
>>
>> For g_hydorder,
>> I get a fatal error when I type the following command:
>> g_hydorder_d -f  file.gro  -s  file.tpr -n waters.ndx -o file1.xpm file2.xpm
>> Error:
>> Internal error in pbc_dx, set pbc has nor been called
>> For more information..
>> 
>>
>> I'm not sure what this means. It seems to be implying that I don't have a 
>> box around my polymer, but the gro file clearly shows that my box is 4.94 x 
>> 4.94 x 4.94. Any ideas?
>>
>
> What is your setting for the pbc keyword in the .mdp file?
>
>>
>> For g_polystat, I'm a bit worried about the persistence lengths that I get 
>> for short polymers. With repeat units smaller than 50 these usually show 
>> "nan" values, that cannot be plotted. From reading the gmx threads I've 
>> found that Nan stands for "Not a Number", but why do these "nan" values 
>> appear and how can I prevent it so that I can read in my results?
>>
>
> This could be an underlying problem related to the above interpretation of
> periodicity.  We don't have enough information to say for sure yet.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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>

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] help with g_hydorder and g_polystat

[Justin Lemkul]

On 4/30/13 9:00 PM, Emmanuel, Alaina wrote:

Hello Justin,

My mdp file shows that the pbc was set to xyz.



Instead of analyzing a coordinate file, does it work with a trajectory? 
Regarding g_polystat and the nan's, what command are you issuing?


-Justin



Kind Regards,

Alaina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin Lemkul [jalem...@vt.edu]
Sent: 30 April 2013 16:10
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat

On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:

Dear All,

I'm fairly new to gromacs and having a bit of problem with the g_hydorder and 
g_polystat. Thanks in advanced for your time.

For g_hydorder,
I get a fatal error when I type the following command:
g_hydorder_d -f  file.gro  -s  file.tpr -n waters.ndx -o file1.xpm file2.xpm
Error:
Internal error in pbc_dx, set pbc has nor been called
For more information..


I'm not sure what this means. It seems to be implying that I don't have a box 
around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 
4.94. Any ideas?



What is your setting for the pbc keyword in the .mdp file?



For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat 
units smaller than 50 these usually show "nan" values, that cannot be plotted. From reading the gmx 
threads I've found that Nan stands for "Not a Number", but why do these "nan" values 
appear and how can I prevent it so that I can read in my results?



This could be an underlying problem related to the above interpretation of
periodicity.  We don't have enough information to say for sure yet.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] help with g_hydorder and g_polystat

[Emmanuel, Alaina]

Hello Justin,

My mdp file shows that the pbc was set to xyz.


Kind Regards,

Alaina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin Lemkul [jalem...@vt.edu]
Sent: 30 April 2013 16:10
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat

On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:
> Dear All,
>
> I'm fairly new to gromacs and having a bit of problem with the g_hydorder and 
> g_polystat. Thanks in advanced for your time.
>
> For g_hydorder,
> I get a fatal error when I type the following command:
> g_hydorder_d -f  file.gro  -s  file.tpr -n waters.ndx -o file1.xpm file2.xpm
> Error:
> Internal error in pbc_dx, set pbc has nor been called
> For more information..
> 
>
> I'm not sure what this means. It seems to be implying that I don't have a box 
> around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 
> x 4.94. Any ideas?
>

What is your setting for the pbc keyword in the .mdp file?

>
> For g_polystat, I'm a bit worried about the persistence lengths that I get 
> for short polymers. With repeat units smaller than 50 these usually show 
> "nan" values, that cannot be plotted. From reading the gmx threads I've found 
> that Nan stands for "Not a Number", but why do these "nan" values appear and 
> how can I prevent it so that I can read in my results?
>

This could be an underlying problem related to the above interpretation of
periodicity.  We don't have enough information to say for sure yet.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] help with g_hydorder and g_polystat

[Emmanuel, Alaina]

Hello Justin, 

My mdp file shows that the pbc was set to xyz.


Kind Regards,

Alaina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin Lemkul [jalem...@vt.edu]
Sent: 30 April 2013 16:10
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat

On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:
> Dear All,
>
> I'm fairly new to gromacs and having a bit of problem with the g_hydorder and 
> g_polystat. Thanks in advanced for your time.
>
> For g_hydorder,
> I get a fatal error when I type the following command:
> g_hydorder_d -f  file.gro  -s  file.tpr -n waters.ndx -o file1.xpm file2.xpm
> Error:
> Internal error in pbc_dx, set pbc has nor been called
> For more information..
> 
>
> I'm not sure what this means. It seems to be implying that I don't have a box 
> around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 
> x 4.94. Any ideas?
>

What is your setting for the pbc keyword in the .mdp file?

>
> For g_polystat, I'm a bit worried about the persistence lengths that I get 
> for short polymers. With repeat units smaller than 50 these usually show 
> "nan" values, that cannot be plotted. From reading the gmx threads I've found 
> that Nan stands for "Not a Number", but why do these "nan" values appear and 
> how can I prevent it so that I can read in my results?
>

This could be an underlying problem related to the above interpretation of
periodicity.  We don't have enough information to say for sure yet.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] help with g_hydorder and g_polystat

[Justin Lemkul]

On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:

Dear All,

I'm fairly new to gromacs and having a bit of problem with the g_hydorder and 
g_polystat. Thanks in advanced for your time.

For g_hydorder,
I get a fatal error when I type the following command:
g_hydorder_d -f  file.gro  -s  file.tpr -n waters.ndx -o file1.xpm file2.xpm
Error:
Internal error in pbc_dx, set pbc has nor been called
For more information..


I'm not sure what this means. It seems to be implying that I don't have a box 
around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 
4.94. Any ideas?



What is your setting for the pbc keyword in the .mdp file?



For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat 
units smaller than 50 these usually show "nan" values, that cannot be plotted. From reading the gmx 
threads I've found that Nan stands for "Not a Number", but why do these "nan" values 
appear and how can I prevent it so that I can read in my results?



This could be an underlying problem related to the above interpretation of 
periodicity.  We don't have enough information to say for sure yet.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] help: load imbalance

[Szilárd Páll]

On Wed, Apr 10, 2013 at 4:50 PM, 申昊  wrote:
> Hello,
>I wanna ask some questions about load imbalance.
> 1> Here are the messages resulted from grompp -f md.mdp -p topol.top -c 
> npt.gro -o md.tpr
>
>NOTE 1 [file md.mdp]:
>   The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid spacing
>
> therefore, i changed the md.mdp as whrited below, then used the command 
> grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr , then there is no NOTE 
> printed. So if i change the cut-offs to 2.0 nm and increase the grid spacing 
> to 0.30, does the calculated results reasonable?

You can shift work between short- and long-range electrostatics by
adjusting the *coulomb* cut-off freely, but *not* the VdW cut-off.

However, 2.0 nm sounds like a *very* long cut-off.

>
> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist   = 2 ; short-range neighborlist cutoff (in nm)
> rcoulomb= 2 ; short-range electrostatic cutoff (in nm)
> rvdw= 2 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range 
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.3   ; grid spacing for FFT
>
> 2> and how about no changes, just simulate it with the original mdp. Is the 
> results still reasonable?  Here are the messages without any changes:
>
> DD  load balancing is limited by minimum cell size in dimension X
> DD  step 2933999  vol min/aver 0.189! load imb.: force 124.7%

You are simply pushing your simulation to the limit of how far it can
be parallelized. As you can see from the above output, to compensate
for the imbalance, the load balancing shrunk DD cells to the extent
that the volume ratio of the smallest and average DD cell size is
0.189, meaning that the smallest DD cells are ~5.3x smaller than the
average cell size - and the run is still *hugely* imbalanced. The "!"
indicates what the line before says, that the DD load-balancing is
limited and can't shrink cells further.

Some aspects that might be limiting your simulation are:
i) running with just a few hundred atoms/core;
ii) running on multiple very different cluster nodes;
iii) using a very inhomogeneous system.

If you're using the group scheme (which i assume you are, otherwise
the automated PP-PME balancing would have kicked in), you should be
able to get better performance at high parallelization with the verlet
scheme.

Cheers,
--
Szilard

>
>Step   Time Lambda
> 2934000 5868.00.0
>
>Energies (kJ/mol)
>   AngleProper Dih. Ryckaert-Bell.  LJ-14 Coulomb-14
> 2.99315e+022.13778e+011.74659e+022.22024e+022.02466e+03
> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
>-1.68074e+02   -2.09809e-01   -1.80294e+03   -3.28155e+03   -2.51074e+03
> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
> 1.69264e+041.44156e+042.95552e+02   -1.33866e-041.51489e+00
>Constr. rmsd
> 2.60082e-05
>
>
>
> --
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Re: [gmx-users] help: load imbalance

[Justin Lemkul]

On Wed, Apr 10, 2013 at 10:50 AM, 申昊  wrote:

> Hello,
>I wanna ask some questions about load imbalance.
> 1> Here are the messages resulted from grompp -f md.mdp -p topol.top -c
> npt.gro -o md.tpr
>
>NOTE 1 [file md.mdp]:
>   The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid spacing
>
> therefore, i changed the md.mdp as whrited below, then used the command
> grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr , then there is no NOTE
> printed. So if i change the cut-offs to 2.0 nm and increase the grid
> spacing to 0.30, does the calculated results reasonable?
>
>
No. You're making ad hoc changes to nonbonded cutoffs (which can completely
invalidate the force field model) and you're making the PME grid less
accurate.

-Justin


> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist   = 2 ; short-range neighborlist cutoff (in nm)
> rcoulomb= 2 ; short-range electrostatic cutoff (in nm)
> rvdw= 2 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.3   ; grid spacing for FFT
>
> 2> and how about no changes, just simulate it with the original mdp. Is
> the results still reasonable?  Here are the messages without any changes:
>
> DD  load balancing is limited by minimum cell size in dimension X
> DD  step 2933999  vol min/aver 0.189! load imb.: force 124.7%
>
>Step   Time Lambda
> 2934000 5868.00.0
>
>Energies (kJ/mol)
>   AngleProper Dih. Ryckaert-Bell.  LJ-14 Coulomb-14
> 2.99315e+022.13778e+011.74659e+022.22024e+022.02466e+03
> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
>-1.68074e+02   -2.09809e-01   -1.80294e+03   -3.28155e+03   -2.51074e+03
> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
> 1.69264e+041.44156e+042.95552e+02   -1.33866e-041.51489e+00
>Constr. rmsd
> 2.60082e-05
>
>
>
> --
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-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] help with chromophore of a GFP

[lloyd riggs]

I had problems having not used gromacs in years a couple years ago.  Try 
running it through with the output as a pdb from pdb2gmx, cut off all headers, 
and you can then just compare the two files in gedit emacs or word and see 
differences.  That might help.  I routinely just keep everything in pdb format 
as its easier than jumping back and forth.


 Original-Nachricht 
> Datum: Thu, 21 Mar 2013 21:43:16 +0100
> Von: Mark Abraham 
> An: Discussion list for GROMACS users 
> Betreff: Re: [gmx-users] help with chromophore of a GFP

> On Thu, Mar 21, 2013 at 4:30 PM, Anna MARABOTTI 
> wrote:
> 
> >
> >
> > Dear Mark,
> >
> > thank you for your message. I'm happy to be on the
> > right track; unfortunately the end point seems to be very far away...
> >
> >
> > I tried to obtain that CFY hydrogens and protein hydrogens are all
> > matching the aminoacids.rtp entry, in order to avoid dealing with
> > aminoacids.hdb. This is what I did:
> >
> > - starting from the pdb file of
> > the protein, I removed CFY entry (prot_noCFY.pdb)
> >
> > - I used pdb2gmx to
> > add H to the protein only: pdb2gmx -f prot_noCFY.pdb -o prot_noCFY_H.pdb
> > -p topol.top
> >
> > - I inserted CFY_H.pdb (obtained with Pymol in a previous
> > passage in which I added H with Pymol to the protein, including CFY)
> > into prot_noCFY_H.pdb, obtaining prot_CFY_H.pdb.
> >
> > In this way, H atoms
> > bound to "regular" residues have been added using Amber99SB, therefore
> > they are compatible with this ff, and atoms of CFY (previously added
> > with Pymol) have the same naming convention in aminoacids.rtp (that I
> > edited using atom types, charges etc. calculated with Antechamber on
> > this molecule coming from Pymol). Obviously, the atom numbering is not
> > sequential: the last atom of V63 (the last "regular" residue before CFY)
> > is numbered 938, the first atom of H68 (the first "regular" residue
> > after CFY) is numbered 939, and the atoms of CFY66 are numbered from 1
> > to 70. Moreover, since the sequence of atoms in aminoacids.rtp is not
> > the same as in the coordinates of CFY (I adapted the sequence of atoms
> > following the format of other residues in aminoacids.rtp), the numbering
> > of CFY in the prot_CFY_H.pdb is not ordered (1-2-3--69-70) but
> > disordered (19-54-20-55...49-50-24-25).
> >
> 
> Seems fine. pdb2gmx is mostly about atom/residue naming. grompp is mostly
> about atom/residue/moleculetype ordering.
> 
> - At this stage, I used
> > pdb2gmx again to create the topol.top file with all coordinates correct:
> >
> >
> > pdb2gmx -f prot_CFY_H.pdb -o prot_complete.gro -p topol.top
> >
> >
> > (selecting amber99sb forcefield and tip3p for water, as recommended
> > option)
> >
> > This is the message error from pdb2gmx:
> >
> > Read 'FLUORESCENT
> > PROTEIN', 3346 atoms
> > Analyzing pdb file
> > Splitting PDB chains based on
> > TER records or changing chain id.
> > There are 1 chains and 0 blocks of
> > water and 218 residues with 3346 atoms
> >
> >  chain #res #atoms
> >  1 'A' 213
> > 3346
> >
> 
> I'd be concerned about the difference in residue count here, but 4.5.4 is
> so old I've no idea whose fault this is.
> 
> 
> > All occupancies are one
> > Opening force field file
> > ./amber99sb.ff/atomtypes.atp
> > Atomtype 1
> > Reading residue database...
> > (amber99sb)
> > Opening force field file
> > ./amber99sb.ff/aminoacids.rtp
> > Residue 94
> > Sorting it all out...
> > Opening
> > force field file ./amber99sb.ff/dna.rtp
> > Residue 110
> > Sorting it all
> > out...
> > Opening force field file ./amber99sb.ff/rna.rtp
> > Residue
> > 126
> > Sorting it all out...
> > Opening force field file
> > ./amber99sb.ff/aminoacids.hdb
> > Opening force field file
> > ./amber99sb.ff/dna.hdb
> > Opening force field file
> > ./amber99sb.ff/rna.hdb
> > Opening force field file
> > ./amber99sb.ff/aminoacids.n.tdb
> > Opening force field file
> > ./amber99sb.ff/aminoacids.c.tdb
> >
> > Processing chain 1 'A' (3346 atoms, 213
> > residues)
> > There are 327 donors and 319 acceptors
> > There are 539 hydrogen
> > bonds
> > Will use HISE for residue 22
> > Will use HISD for residue 38
> > Will use
> > HISE for residue 62
> > Will use HISE for residue 68
> > Will use HISD for
>

Re: [gmx-users] help with chromophore of a GFP

[Justin Lemkul]

119 NE21803 1.688 0.976 0.584
1.078
  MET135 SD2041 1.057 1.365 2.661 2.490 2.119
  MET162 SD2439 1.878
0.871 1.805 2.246 1.520 1.861
  HIS172 NE22588 1.721 1.401 2.829 2.860
2.359 1.067 1.342
  CYS174 SG2623 1.694 0.725 2.140 2.152 1.681 1.297
0.745
  MET189 SD2891 3.547 2.310 1.858 1.893 1.980 3.627 2.290
  HIS193
NE22942 3.076 1.890 1.639 2.197 1.760 3.221 1.547
  HIS197 NE23011 2.229
1.149 1.407 2.078 1.323 2.401 0.676
  HIS217 NE23329 3.146 2.112 2.205
2.935 2.272 3.263 1.402
  HIS172 CYS174 MET189 HIS193 HIS197
  NE22588
SG2623 SD2891 NE22942 NE23011
  CYS174 SG2623 0.826
  MET189 SD2891 3.417
2.599
  HIS193 NE22942 2.831 2.079 1.020
  HIS197 NE23011 2.011 1.324
1.766 0.939
  HIS217 NE23329 2.629 2.068 1.936 0.946 1.003
Opening force
field file ./amber99sb.ff/aminoacids.arn
Opening force field file
./amber99sb.ff/dna.arn
Opening force field file
./amber99sb.ff/rna.arn
Checking for duplicate atoms
Now there are
3345 atoms. Deleted 1 duplicates.



That also looks suspicious.



Now there are 213 residues with 3345
atoms
Making bonds...
Warning: Long Bond (988-989 = 0.453624
nm)



That seems like it might be a peptide bond bridging a "gap" where pdb2gmx
was unable to recognize the intervening content as a peptide residue.




WARNING: atom O1 is missing in residue CFY 66 in the pdb
file

---
Program
pdb2gmx_d, VERSION 4.5.4
Source code file: pdb2top.c, line: 1463

Fatal
error:
There were 1 missing atoms in molecule Protein_chain_A, if you
want to use this incomplete topology anyhow, use the option -missing
For
more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors

The
strange thing is that I checked for this error, but atom O1 in residue
CFY66 is present BOTH in the starting .pdb file (the one I used for
pdb2gmx) AND in the aminoacids.rtp file I checked 4 or 5 times,
every time erasing the old file, checking the file IMMEDIATELY BEFORE
submitting it to pdb2gmx. All atoms present in aminoacids.rtp for CFY
residue are also present in the .pdb file and vice versa, and I am sure
I did not make the stupid error of naming the atom 01 (zero-one) instead
of O1 (o-one).

I suspect that this atom is the one which is deleted
because recognized as duplicated, but I'm not sure about it and I don't
know how to check it. I am sure there are no duplicated atoms in CFY.


I feel like this is a "fake" error message (i.e.: there is an error in
my files, but it is not the one that is reported in the message:
probably a problem occur around this atom, but it is not exactly ON this
atom). However, I am not able to find errors.



Hmm that seems weird. Justin's theory sounds plausible, but I haven't seen
someone stumble on that before. Also plausible is that pdb2gmx thinks your
CFY is a disconnected part of the chain and needs terminating (which might
happen with an oxygen named O1?).



I stumbled across it when working with the GFP chromophore a while back :)

http://redmine.gromacs.org/issues/567

Still technically an open "bug," though I agree that it's really expected 
behavior, provided one knows how pdb2gmx works, which involves lots of steps, of 
course.


-Justin


It's possible there's buggy behaviour here that has been fixed in the two
years since that code was released. There certainly has been an upgrade of
the "is this really a new chain" machinery. Unless you have a strong
scientific reason to keep 4.5.4, I'd switch to 4.6.1 (or 4.5.6 if you
really have to keep 4.5). If Justin's fix doesn't work, and you have
problems with a more recent version, then we can look closer.



BTW the "long bond" of
the other warning message is not involving residue CFY.



Yeah, but my bet is those atoms are the C-terminus and N-terminus of the
fragments that should form peptide bonds to CFY.

Mark



Any help is
welcome

Thank you so much.

Anna

Il 21.03.2013 12:00
gmx-users-requ...@gromacs.org ha scritto:


Dear gmx-users, it's

about two weeks that I'm trying to solve this problem, and I can't, so
I'm asking your help. I want to do some MD simulations on a protein of
the family of green fluorescent protein. This protein, as you know, has
a chromophore (CFY) derived from four residues of the protein
(F64-C65-Y66-G67) and covalently bound to the rest of the protein chain.
How to parametrize this object, since it is not recognized by pdb2gmx? I
looked at the gmx-users list and the suggestion was to create a new
entry in the .rtp file of the selected forcefield.


Indeed, this

kind of problem is most easily solved by making a new

"residue" that

contains the whole chromophore, such that it links to its

neighbours

with normal peptide links.

-- Message: 5

Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham
 Subject: Re: [gmx-users]

Re: [gmx-users] help with chromophore of a GFP

[Mark Abraham]

9
> 2.121 0.993
>  MET162 SD2439 2.521 1.976 1.656 2.412 1.855 1.543 2.264
>
> HIS172 NE22588 3.632 2.949 1.894 1.657 2.872 2.338 1.945
>  CYS174 SG2623
> 2.968 2.372 1.452 1.861 2.428 1.848 1.924
>  MET189 SD2891 2.167 2.379
> 2.736 4.000 2.754 2.569 3.722
>  HIS193 NE22942 2.003 2.001 2.490 3.686
> 2.049 2.075 3.396
>  HIS197 NE23011 2.012 1.634 1.830 2.896 1.554 1.426
> 2.614
>  HIS217 NE23329 2.545 2.376 2.831 3.805 2.039 2.305 3.575
>  MET53
> HIS62 HIS68 HIS109 HIS119 MET135 MET162
>  SD777 NE2917 NE21002 NE21638
> NE21803 SD2041 SD2439
>  HIS62 NE2917 1.363
>  HIS68 NE21002 2.107 1.482
>
> HIS109 NE21638 2.365 1.568 1.372
>  HIS119 NE21803 1.688 0.976 0.584
> 1.078
>  MET135 SD2041 1.057 1.365 2.661 2.490 2.119
>  MET162 SD2439 1.878
> 0.871 1.805 2.246 1.520 1.861
>  HIS172 NE22588 1.721 1.401 2.829 2.860
> 2.359 1.067 1.342
>  CYS174 SG2623 1.694 0.725 2.140 2.152 1.681 1.297
> 0.745
>  MET189 SD2891 3.547 2.310 1.858 1.893 1.980 3.627 2.290
>  HIS193
> NE22942 3.076 1.890 1.639 2.197 1.760 3.221 1.547
>  HIS197 NE23011 2.229
> 1.149 1.407 2.078 1.323 2.401 0.676
>  HIS217 NE23329 3.146 2.112 2.205
> 2.935 2.272 3.263 1.402
>  HIS172 CYS174 MET189 HIS193 HIS197
>  NE22588
> SG2623 SD2891 NE22942 NE23011
>  CYS174 SG2623 0.826
>  MET189 SD2891 3.417
> 2.599
>  HIS193 NE22942 2.831 2.079 1.020
>  HIS197 NE23011 2.011 1.324
> 1.766 0.939
>  HIS217 NE23329 2.629 2.068 1.936 0.946 1.003
> Opening force
> field file ./amber99sb.ff/aminoacids.arn
> Opening force field file
> ./amber99sb.ff/dna.arn
> Opening force field file
> ./amber99sb.ff/rna.arn
> Checking for duplicate atoms
> Now there are
> 3345 atoms. Deleted 1 duplicates.
>

That also looks suspicious.


> Now there are 213 residues with 3345
> atoms
> Making bonds...
> Warning: Long Bond (988-989 = 0.453624
> nm)
>

That seems like it might be a peptide bond bridging a "gap" where pdb2gmx
was unable to recognize the intervening content as a peptide residue.


>
> WARNING: atom O1 is missing in residue CFY 66 in the pdb
> file
>
> ---
> Program
> pdb2gmx_d, VERSION 4.5.4
> Source code file: pdb2top.c, line: 1463
>
> Fatal
> error:
> There were 1 missing atoms in molecule Protein_chain_A, if you
> want to use this incomplete topology anyhow, use the option -missing
> For
> more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> The
> strange thing is that I checked for this error, but atom O1 in residue
> CFY66 is present BOTH in the starting .pdb file (the one I used for
> pdb2gmx) AND in the aminoacids.rtp file I checked 4 or 5 times,
> every time erasing the old file, checking the file IMMEDIATELY BEFORE
> submitting it to pdb2gmx. All atoms present in aminoacids.rtp for CFY
> residue are also present in the .pdb file and vice versa, and I am sure
> I did not make the stupid error of naming the atom 01 (zero-one) instead
> of O1 (o-one).
>
> I suspect that this atom is the one which is deleted
> because recognized as duplicated, but I'm not sure about it and I don't
> know how to check it. I am sure there are no duplicated atoms in CFY.
>
>
> I feel like this is a "fake" error message (i.e.: there is an error in
> my files, but it is not the one that is reported in the message:
> probably a problem occur around this atom, but it is not exactly ON this
> atom). However, I am not able to find errors.
>

Hmm that seems weird. Justin's theory sounds plausible, but I haven't seen
someone stumble on that before. Also plausible is that pdb2gmx thinks your
CFY is a disconnected part of the chain and needs terminating (which might
happen with an oxygen named O1?).

It's possible there's buggy behaviour here that has been fixed in the two
years since that code was released. There certainly has been an upgrade of
the "is this really a new chain" machinery. Unless you have a strong
scientific reason to keep 4.5.4, I'd switch to 4.6.1 (or 4.5.6 if you
really have to keep 4.5). If Justin's fix doesn't work, and you have
problems with a more recent version, then we can look closer.


> BTW the "long bond" of
> the other warning message is not involving residue CFY.
>

Yeah, but my bet is those atoms are the C-terminus and N-terminus of the
fragments that should form peptide bonds to CFY.

Mark


> Any help is
> welcome
>
> Thank you so much.
>
> Anna
>
> Il 21.03.2013 12:00
> gmx-users-requ...@gromacs.org ha scritto:
>
> >> Dear gmx-users, it's
> about two weeks that I'm trying

Re: [gmx-users] help with chromophore of a GFP

[Justin Lemkul]

.379
> 2.736 4.000 2.754 2.569 3.722
>  HIS193 NE22942 2.003 2.001 2.490 3.686
> 2.049 2.075 3.396
>  HIS197 NE23011 2.012 1.634 1.830 2.896 1.554 1.426
> 2.614
>  HIS217 NE23329 2.545 2.376 2.831 3.805 2.039 2.305 3.575
>  MET53
> HIS62 HIS68 HIS109 HIS119 MET135 MET162
>  SD777 NE2917 NE21002 NE21638
> NE21803 SD2041 SD2439
>  HIS62 NE2917 1.363
>  HIS68 NE21002 2.107 1.482
>
> HIS109 NE21638 2.365 1.568 1.372
>  HIS119 NE21803 1.688 0.976 0.584
> 1.078
>  MET135 SD2041 1.057 1.365 2.661 2.490 2.119
>  MET162 SD2439 1.878
> 0.871 1.805 2.246 1.520 1.861
>  HIS172 NE22588 1.721 1.401 2.829 2.860
> 2.359 1.067 1.342
>  CYS174 SG2623 1.694 0.725 2.140 2.152 1.681 1.297
> 0.745
>  MET189 SD2891 3.547 2.310 1.858 1.893 1.980 3.627 2.290
>  HIS193
> NE22942 3.076 1.890 1.639 2.197 1.760 3.221 1.547
>  HIS197 NE23011 2.229
> 1.149 1.407 2.078 1.323 2.401 0.676
>  HIS217 NE23329 3.146 2.112 2.205
> 2.935 2.272 3.263 1.402
>  HIS172 CYS174 MET189 HIS193 HIS197
>  NE22588
> SG2623 SD2891 NE22942 NE23011
>  CYS174 SG2623 0.826
>  MET189 SD2891 3.417
> 2.599
>  HIS193 NE22942 2.831 2.079 1.020
>  HIS197 NE23011 2.011 1.324
> 1.766 0.939
>  HIS217 NE23329 2.629 2.068 1.936 0.946 1.003
> Opening force
> field file ./amber99sb.ff/aminoacids.arn
> Opening force field file
> ./amber99sb.ff/dna.arn
> Opening force field file
> ./amber99sb.ff/rna.arn
> Checking for duplicate atoms
> Now there are
> 3345 atoms. Deleted 1 duplicates.
> Now there are 213 residues with 3345
> atoms
> Making bonds...
> Warning: Long Bond (988-989 = 0.453624
> nm)
>
> WARNING: atom O1 is missing in residue CFY 66 in the pdb
> file
>
> ---
> Program
> pdb2gmx_d, VERSION 4.5.4
> Source code file: pdb2top.c, line: 1463
>
> Fatal
> error:
> There were 1 missing atoms in molecule Protein_chain_A, if you
> want to use this incomplete topology anyhow, use the option -missing
> For
> more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> The
> strange thing is that I checked for this error, but atom O1 in residue
> CFY66 is present BOTH in the starting .pdb file (the one I used for
> pdb2gmx) AND in the aminoacids.rtp file I checked 4 or 5 times,
> every time erasing the old file, checking the file IMMEDIATELY BEFORE
> submitting it to pdb2gmx. All atoms present in aminoacids.rtp for CFY
> residue are also present in the .pdb file and vice versa, and I am sure
> I did not make the stupid error of naming the atom 01 (zero-one) instead
> of O1 (o-one).
>
> I suspect that this atom is the one which is deleted
> because recognized as duplicated, but I'm not sure about it and I don't
> know how to check it. I am sure there are no duplicated atoms in CFY.
>
>
> I feel like this is a "fake" error message (i.e.: there is an error in
> my files, but it is not the one that is reported in the message:
> probably a problem occur around this atom, but it is not exactly ON this
> atom). However, I am not able to find errors.
>
>
This is indeed a false error. It comes from the fact that pdb2gmx
interprets anything named O1 or O2 as C-terminal atoms. Use any other name
you like aside from O1 or O2.

-Justin


> BTW the "long bond" of
> the other warning message is not involving residue CFY.
>
> Any help is
> welcome
>
> Thank you so much.
>
> Anna
>
> Il 21.03.2013 12:00
> gmx-users-requ...@gromacs.org ha scritto:
>
> >> Dear gmx-users, it's
> about two weeks that I'm trying to solve this problem, and I can't, so
> I'm asking your help. I want to do some MD simulations on a protein of
> the family of green fluorescent protein. This protein, as you know, has
> a chromophore (CFY) derived from four residues of the protein
> (F64-C65-Y66-G67) and covalently bound to the rest of the protein chain.
> How to parametrize this object, since it is not recognized by pdb2gmx? I
> looked at the gmx-users list and the suggestion was to create a new
> entry in the .rtp file of the selected forcefield.
> >
> > Indeed, this
> kind of problem is most easily solved by making a new
> > "residue" that
> contains the whole chromophore, such that it links to its
> > neighbours
> with normal peptide links.
> > -- Message: 5
> Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham
>  Subject: Re: [gmx-users] help with
> chromophore of a GFP To: Discussion list for GROMACS users
>  Message-ID:
> 
> Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar 20, 2

Re: [gmx-users] help with chromophore of a GFP

[Anna MARABOTTI]

 HIS197 NE23011 2.229
1.149 1.407 2.078 1.323 2.401 0.676
 HIS217 NE23329 3.146 2.112 2.205
2.935 2.272 3.263 1.402
 HIS172 CYS174 MET189 HIS193 HIS197
 NE22588
SG2623 SD2891 NE22942 NE23011
 CYS174 SG2623 0.826
 MET189 SD2891 3.417
2.599
 HIS193 NE22942 2.831 2.079 1.020
 HIS197 NE23011 2.011 1.324
1.766 0.939
 HIS217 NE23329 2.629 2.068 1.936 0.946 1.003
Opening force
field file ./amber99sb.ff/aminoacids.arn
Opening force field file
./amber99sb.ff/dna.arn
Opening force field file
./amber99sb.ff/rna.arn
Checking for duplicate atoms
Now there are
3345 atoms. Deleted 1 duplicates.
Now there are 213 residues with 3345
atoms
Making bonds...
Warning: Long Bond (988-989 = 0.453624
nm)

WARNING: atom O1 is missing in residue CFY 66 in the pdb
file

---
Program
pdb2gmx_d, VERSION 4.5.4
Source code file: pdb2top.c, line: 1463

Fatal
error:
There were 1 missing atoms in molecule Protein_chain_A, if you
want to use this incomplete topology anyhow, use the option -missing
For
more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors 

The
strange thing is that I checked for this error, but atom O1 in residue
CFY66 is present BOTH in the starting .pdb file (the one I used for
pdb2gmx) AND in the aminoacids.rtp file I checked 4 or 5 times,
every time erasing the old file, checking the file IMMEDIATELY BEFORE
submitting it to pdb2gmx. All atoms present in aminoacids.rtp for CFY
residue are also present in the .pdb file and vice versa, and I am sure
I did not make the stupid error of naming the atom 01 (zero-one) instead
of O1 (o-one). 

I suspect that this atom is the one which is deleted
because recognized as duplicated, but I'm not sure about it and I don't
know how to check it. I am sure there are no duplicated atoms in CFY.


I feel like this is a "fake" error message (i.e.: there is an error in
my files, but it is not the one that is reported in the message:
probably a problem occur around this atom, but it is not exactly ON this
atom). However, I am not able to find errors. 

BTW the "long bond" of
the other warning message is not involving residue CFY. 

Any help is
welcome 

Thank you so much. 

Anna

Il 21.03.2013 12:00
gmx-users-requ...@gromacs.org ha scritto: 

>> Dear gmx-users, it's
about two weeks that I'm trying to solve this problem, and I can't, so
I'm asking your help. I want to do some MD simulations on a protein of
the family of green fluorescent protein. This protein, as you know, has
a chromophore (CFY) derived from four residues of the protein
(F64-C65-Y66-G67) and covalently bound to the rest of the protein chain.
How to parametrize this object, since it is not recognized by pdb2gmx? I
looked at the gmx-users list and the suggestion was to create a new
entry in the .rtp file of the selected forcefield.
> 
> Indeed, this
kind of problem is most easily solved by making a new
> "residue" that
contains the whole chromophore, such that it links to its
> neighbours
with normal peptide links.
> -- Message: 5
Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham
 Subject: Re: [gmx-users] help with
chromophore of a GFP To: Discussion list for GROMACS users
 Message-ID:

Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar 20, 2013 at
6:01 PM, Anna MARABOTTI  wrote: 
> 
>> I
decided to use Amber99SB since it seemed the better for my scope, then I
start trying to parameterize it. This is what I did: * I used Pymol to
add H to my pdb file, since I want to use an all H forcefield and since
Antechamber (see below) does not work without H * I extracted the
segment V63-CFY-H68 from my .pdb file. I did this since, when I
extracted CFY only, I had problems with the terminals * Following the
Antechamber tutorial, I used Antechamber (using the traditional Amber
force field, not GAFF) to calculate charges and to assign atom types to
this segment. * I used these calculated parameters in order to add the
CFY residue to aminoacids.rtp in amber99sb.ff directory. * I tried to
modify also aminoacids.hdb, but since it seemed too complicated to me, I
decided to keep it unchanged, and to give pdb2gmx the protein with H
already present * No need to add new atom/bond types to ffbonded.itp and
ffnonbonded.itp: they seem all present. Since CFY is bound to the rest
of protein with common peptide bonds, I did not change specbond.dat
either. * I added CFY in residuetypes.dat with the specification
"Protein" In my opinion, all was ready to go, instead... When I launched
pdb2gmx to my protein with H added by PyMol, I got immediately an error:
Fatal error: Atom H01 in residue SER 3 was not found in rtp entry NSER
with 13 atoms while sorting atoms. For a hydrogen, this can be a
different protonation state, or it might have had a different number in
the PDB file and was rebuilt (

Re: [gmx-users] help with chromophore of a GFP

[Mark Abraham]

On Wed, Mar 20, 2013 at 6:01 PM, Anna MARABOTTI  wrote:

>
>
> Dear gmx-users,
>
> it's about two weeks that I'm trying to solve this
> problem, and I can't, so I'm asking your help.
>
> I want to do some MD
> simulations on a protein of the family of green fluorescent protein.
> This protein, as you know, has a chromophore (CFY) derived from four
> residues of the protein (F64-C65-Y66-G67) and covalently bound to the
> rest of the protein chain. How to parametrize this object, since it is
> not recognized by pdb2gmx? I looked at the gmx-users list and the
> suggestion was to create a new entry in the .rtp file of the selected
> forcefield.


Indeed, this kind of problem is most easily solved by making a new
"residue" that contains the whole chromophore, such that it links to its
neighbours with normal peptide links.


> I decided to use Amber99SB since it seemed the better for my
> scope, then I start trying to parameterize it. This is what I did:
>
> *
>
>
> I used Pymol to add H to my pdb file, since I want to use an all H
> forcefield and since Antechamber (see below) does not work without H
> *
>
>
> I extracted the segment V63-CFY-H68 from my .pdb file. I did this
> since, when I extracted CFY only, I had problems with the terminals
> *
>
>
> Following the Antechamber tutorial, I used Antechamber (using the
> traditional Amber force field, not GAFF) to calculate charges and to
> assign atom types to this segment.
> *
>
> I used these calculated
> parameters in order to add the CFY residue to aminoacids.rtp in
> amber99sb.ff directory.
> *
>
> I tried to modify also aminoacids.hdb, but
> since it seemed too complicated to me, I decided to keep it unchanged,
> and to give pdb2gmx the protein with H already present
> *
>
> No need to
> add new atom/bond types to ffbonded.itp and ffnonbonded.itp: they seem
> all present. Since CFY is bound to the rest of protein with common
> peptide bonds, I did not change specbond.dat either.
> *
>
> I added CFY
> in residuetypes.dat with the specification "Protein"
>
> In my opinion,
> all was ready to go, instead...
>
> When I launched pdb2gmx to my protein
> with H added by PyMol, I got immediately an error:
>
> Fatal error:
>
> Atom
> H01 in residue SER 3 was not found in rtp entry NSER with 13 atoms
>
>
> while sorting atoms.
>
> For a hydrogen, this can be a different
> protonation state, or it
>
> might have had a different number in the PDB
> file and was rebuilt
>
> (it might for instance have been H3, and we only
> expected H1 & H2).
>
> Note that hydrogens might have been added to the
> entry for the N-terminus.
>
> Remove this hydrogen or choose a different
> protonation state to solve it.
>
> Option -ignh will ignore all hydrogens
> in the input.
>
> For more information and tips for troubleshooting,
> please check the GROMACS
>
> website at
> http://www.gromacs.org/Documentation/Errors [1]
>
> >From this error I
> understand that:
>
> *
>
> the code for H in PyMol is different from the
> code for H in Amber (read from aminoacids.rtp); in order to correct this
> error, I should add -ignh in order to ignore H in input.
>

pdb2gmx has to be able to make sense of the atom naming. There are lots of
different conventions for how to name atoms, particularly hydrogen atoms.
pdb2gmx can't possibly encode the logic to convert all of those
conventions. So the path of least resistance can be to ignore hydrogens and
regenerate them according to the generation rules.

However, you can just rename them in the input file so that pdb2gmx
understands your meaning. The NSER entry in the .rtp file shows you the
names pdb2gmx expects. If you edit the names of those hydrogen atoms
(probably H01, H02, H03) in your input coordinate file accordingly (to H1,
H2, H3), things will be fine. Be sure you don't break the required column
formatting of the coordinate file!

*
>
> If I add
> -ignh, all the H of CFY will be ignored too, and I will not be able to
> add them since I did not modify aminoacids.hdb
> *
>
> since I made
> calculations on CFY with H added by PyMol, probably also my codes for H
> will be wrong.
>

Your atom names for CFY in the .rtp and the input coordinate file will have
to match. How you want to achieve that is up to you.


> *
>
> If I use "reduce" (the Amber tool to add H, as
> suggested by the tutorial) to add H to my protein, it does not add H to
> CFY because it complaints that the residue is not in HETATM connection
> database (but the record CONECT is present in .pdb file). If I add H to
> CFY alone, I have problems with the terminals.
>
> My question is,
> obviously: how can I parameterize this chromophore correctly? Please
> give me, if possible, some step-by-step indications on what to do. I
> made dozens of trials, ALL with errors, and I really do not know how to
> do.
>

You're very much on the right track.

Your decision to use Pymol to generate main chain hydroge

Re: [gmx-users] help with chromophore of a GFP

[Anna Marabotti]

Dear Justin,
there is not a "unique" GFP chromophore, the chromophore I am dealing 
with is not the same for which CHARMM parameters have been published (I 
am aware of CHARMM parameters for p-hydroxybenzylideneimidazolinone 
chromophore of green fluorescent protein published by Reuter et al 2002, 
of OPLS-AA parameters for DsRed fluorescent protein chromophore as a 
residue of [(4
cis)
2
[(1
cis)
4
 
amino
4
oxobutanimidoyl]
4
(4
hydroxybenzylidene)
5
oxo
4,5
dihydro
1H
imidazol
1
yl]acetic 
acid, of other parameters of other GFP chromophores), but mine is 
different: is of the same family of proteins, but different residues are 
involved and different heterocycles are generated.


Since I have to recalculate parameters, I chose Amber ff because I 
already used it and I have tools to calculate Amber parameters, whereas 
I have no tools to calculate CHARMM parameters. In a preliminary assay, 
I tried to do the same parameterization using Gromos ff and PRODRG to 
obtain parameters and topology (apart from the fact that charges are 
probably wrong), but I experimented the same problem.


I am talking not only about the problem of obtaining parameters for this 
particular chromophore, mine is a more general question: how to deal 
with a "HETATM" entry which is not a ligand, but it's a part of the 
protein chain? I tried to follow indications to make a new .rtp entry in 
the GROMACS HowTo's, probably my problem would be solved if I would be 
able to modify the aminoacids.hdb file, but this is not a simple 
modification of a residue (eg. an oxidised Met or a methylation of a 
Lys), this is a profound modification of four residues, so how can I 
deal with this? I had a look at the .hdb file, but hydrogens I can see 
are typical for amino acids residues and I cannot find any suggestions 
on how to treat hydrogens that are bound to a "residue" which is so 
different from classic standard residues. Has anyone made this before (I 
am sure yes)? Could you please give some suggestions?


Thank you very much
Anna

__
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Ponte don Melillo
84084 Fisciano (SA)
Italy
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabo...@unisa.it
Skype: annam1972

"When a man with a gun meets a man with a pen, the man with the gun is a dead 
man"
(Roberto Benigni, about Roberto Saviano)

Il 21/03/2013 06:37, gmx-users-requ...@gromacs.org ha scritto:
Message: 3 Date: Wed, 20 Mar 2013 13:05:08 -0400 From: Justin Lemkul 
 Subject: Re: [gmx-users] help with chromophore of a 
GFP To: Discussion list for GROMACS users  
Message-ID: 
 
Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar 20, 2013 at 
1:01 PM, Anna MARABOTTI  wrote:

>
>
>Dear gmx-users,
>
>it's about two weeks that I'm trying to solve this
>problem, and I can't, so I'm asking your help.
>
>I want to do some MD
>simulations on a protein of the family of green fluorescent protein.
>This protein, as you know, has a chromophore (CFY) derived from four
>residues of the protein (F64-C65-Y66-G67) and covalently bound to the
>rest of the protein chain. How to parametrize this object, since it is
>not recognized by pdb2gmx? I looked at the gmx-users list and the
>suggestion was to create a new entry in the .rtp file of the selected
>forcefield. I decided to use Amber99SB since it seemed the better for my
>scope, then I start trying to parameterize it. This is what I did:
>
> *
>
>
>I used Pymol to add H to my pdb file, since I want to use an all H
>forcefield and since Antechamber (see below) does not work without H
> *
>
>
>I extracted the segment V63-CFY-H68 from my .pdb file. I did this
>since, when I extracted CFY only, I had problems with the terminals
> *
>
>
>Following the Antechamber tutorial, I used Antechamber (using the
>traditional Amber force field, not GAFF) to calculate charges and to
>assign atom types to this segment.
> *
>
>I used these calculated
>parameters in order to add the CFY residue to aminoacids.rtp in
>amber99sb.ff directory.
> *
>
>I tried to modify also aminoacids.hdb, but
>since it seemed too complicated to me, I decided to keep it unchanged,
>and to give pdb2gmx the protein with H already present
> *
>
>No need to
>add new atom/bond types to ffbonded.itp and ffnonbonded.itp: they seem
>all present. Since CFY is bound to the rest of protein with common
>peptide bonds, I did not change specbond.dat either.
> *
>
>I added CFY
>in residuetypes.dat with the specification "Protein"
>
>In my opinion,
>all was ready to go, instead...
>
>When I launched pdb2gmx to my protein
>with H added by PyMol, I got

Re: [gmx-users] help with chromophore of a GFP

[Justin Lemkul]

On Wed, Mar 20, 2013 at 1:01 PM, Anna MARABOTTI  wrote:

>
>
> Dear gmx-users,
>
> it's about two weeks that I'm trying to solve this
> problem, and I can't, so I'm asking your help.
>
> I want to do some MD
> simulations on a protein of the family of green fluorescent protein.
> This protein, as you know, has a chromophore (CFY) derived from four
> residues of the protein (F64-C65-Y66-G67) and covalently bound to the
> rest of the protein chain. How to parametrize this object, since it is
> not recognized by pdb2gmx? I looked at the gmx-users list and the
> suggestion was to create a new entry in the .rtp file of the selected
> forcefield. I decided to use Amber99SB since it seemed the better for my
> scope, then I start trying to parameterize it. This is what I did:
>
> *
>
>
> I used Pymol to add H to my pdb file, since I want to use an all H
> forcefield and since Antechamber (see below) does not work without H
> *
>
>
> I extracted the segment V63-CFY-H68 from my .pdb file. I did this
> since, when I extracted CFY only, I had problems with the terminals
> *
>
>
> Following the Antechamber tutorial, I used Antechamber (using the
> traditional Amber force field, not GAFF) to calculate charges and to
> assign atom types to this segment.
> *
>
> I used these calculated
> parameters in order to add the CFY residue to aminoacids.rtp in
> amber99sb.ff directory.
> *
>
> I tried to modify also aminoacids.hdb, but
> since it seemed too complicated to me, I decided to keep it unchanged,
> and to give pdb2gmx the protein with H already present
> *
>
> No need to
> add new atom/bond types to ffbonded.itp and ffnonbonded.itp: they seem
> all present. Since CFY is bound to the rest of protein with common
> peptide bonds, I did not change specbond.dat either.
> *
>
> I added CFY
> in residuetypes.dat with the specification "Protein"
>
> In my opinion,
> all was ready to go, instead...
>
> When I launched pdb2gmx to my protein
> with H added by PyMol, I got immediately an error:
>
> Fatal error:
>
> Atom
> H01 in residue SER 3 was not found in rtp entry NSER with 13 atoms
>
>
> while sorting atoms.
>
> For a hydrogen, this can be a different
> protonation state, or it
>
> might have had a different number in the PDB
> file and was rebuilt
>
> (it might for instance have been H3, and we only
> expected H1 & H2).
>
> Note that hydrogens might have been added to the
> entry for the N-terminus.
>
> Remove this hydrogen or choose a different
> protonation state to solve it.
>
> Option -ignh will ignore all hydrogens
> in the input.
>
> For more information and tips for troubleshooting,
> please check the GROMACS
>
> website at
> http://www.gromacs.org/Documentation/Errors [1]
>
> >From this error I
> understand that:
>
> *
>
> the code for H in PyMol is different from the
> code for H in Amber (read from aminoacids.rtp); in order to correct this
> error, I should add -ignh in order to ignore H in input.
> *
>
> If I add
> -ignh, all the H of CFY will be ignored too, and I will not be able to
> add them since I did not modify aminoacids.hdb
> *
>
> since I made
> calculations on CFY with H added by PyMol, probably also my codes for H
> will be wrong.
> *
>
> If I use "reduce" (the Amber tool to add H, as
> suggested by the tutorial) to add H to my protein, it does not add H to
> CFY because it complaints that the residue is not in HETATM connection
> database (but the record CONECT is present in .pdb file). If I add H to
> CFY alone, I have problems with the terminals.
>
> My question is,
> obviously: how can I parameterize this chromophore correctly? Please
> give me, if possible, some step-by-step indications on what to do. I
> made dozens of trials, ALL with errors, and I really do not know how to
> do.
>
>
There are parameters published for the GFP chromophore under the CHARMM
force field; is there some reason those are unsuitable?  No need to
reinvent the wheel.  With the published parameters, one simply needs to
create an .rtp entry and pdb2gmx runs fine, no need to mess with
antechamber, PyMOL, etc.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] help

[Justin Lemkul]

On 2/26/13 7:46 AM, Sjøli Stian wrote:

dear gmx-users,
this is a stupid question (and partially a test of use). I cant find any 
information on how to use/modify maxvarn as a parameter for grompp. Can you 
point to examples or literature?



Consider the help text:

-maxwarn int0   Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems

This tells you the name of the option, that it takes an integer argument, and 
that the default value is zero (i.e., do not bypass warnings).  If you want to 
bypass one warning:


grompp -maxwarn 1

Note that one should not normally use this option.  There is one case I can 
think of where it is useful, and about a thousand others where it will cause 
unreliable simulations.  If grompp is telling you something is wrong, heed its 
warning(s).


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] help with building DNA in gromacs

[יוכבד]

Hi Steven

I'm running simulations on DNA structures using the amber99sb-ildn FF. I
had no problem generating .top and .gro files
I might be able to help if you are interested.
send me the PDB file.

Yocheved

On Sun, Jan 20, 2013 at 10:57 PM, Tom  wrote:

> Dear Gromacs User
>
> I built DNA with the pdb file and *mol2
> But when I used pdb2gmx to obtain *top file, pdb2gmx give error
> report when I chose charmm27:
> ---
> Program pdb2gmx, VERSION 4.5.5
> Source code file: resall.c, line: 581
> Fatal error:
> Residue 'T' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Also can not work for the other forcefileds.
> Why for simple DNA is so difficult to build topology file?
> Is there any toolbox to help buld the top file?
>
> Thanks,
>
> Steven
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] help with building DNA in gromacs

[Justin Lemkul]

On 1/20/13 3:57 PM, Tom wrote:

Dear Gromacs User

I built DNA with the pdb file and *mol2
But when I used pdb2gmx to obtain *top file, pdb2gmx give error
report when I chose charmm27:
---
Program pdb2gmx, VERSION 4.5.5
Source code file: resall.c, line: 581
Fatal error:
Residue 'T' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Also can not work for the other forcefileds.
Why for simple DNA is so difficult to build topology file?


Your residue names need to match the force field's expectations.  That much is 
true for any molecule passed to pdb2gmx - protein, DNA, RNA, whatever.  Consult 
the .rtp file for your chosen force field and edit your coordinate file accordingly.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] help with improper angle in gmx

[Justin Lemkul]

On 1/7/13 6:11 PM, Tom wrote:

Dear Gromacs Users

I want to use harmonic type of improper angle potential with opls-aa

The manu seems not clear.

Can anyone give an small example about the format in *rtp file
and ffbond.itp file?



The names of improper_*_*_*_* tell you to what improper the parameters apply. 
X, Y, and Z are used to indicate any atom.  The only other atoms used are the 
types that can be used in those positions, i.e. O_C_X_Y is the improper about a 
carbonyl, while Z_N_X_Y is used in amide groups (peptide bonds).


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] help

[Justin Lemkul]

On 12/2/12 2:17 AM, 申昊 wrote:

Hi everyone，
   I am a new one on using gromacs. Now I have some problems.
   [1] I want using g_analyze to calculate the self-ACF with the dist.xvg 
resulted from g_dist, the file nameddist.xvg consists two lists of 
time(ns) and distance(nm), respectively.
  (a)why the result shows a combination of four curves? Is there any 
options missed (for plotting the only one curve)?


The dist.xvg file from g_dist has the total distance, then the x, y, and z 
components of that distance.  If you want only the total distance for analysis, 
you have to parse that yourself with a script or suitable awk command.



  (b)I noticed that some regions of the curves were negative, is it 
correct? Whether the calculation ofACFs is according to the 
integral methods or cosine methods?


You can have negative values within the (x,y,z) portion of dist.xvg since the 
components are vectors.


ACF calculations are discussed in the manual, section 8.5.


   [2] Does the tetrahedral order parameter of water can be calculated by 
g_order? How to generate this   parameter?


g_order is for lipids.


   [3] Virtual sites are useful in some simulations. I read the tutorial on the 
web site of 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/. What i 
really care about is whether the virtual sites should always be used for gas 
state. I mean, in solutions, the oscillations of the angles are rational.



My virtual site tutorial is one example of special uses of virtual sites dealing 
solely with linear molecules.  Virtual sites can be useful in a number of 
situations.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] help

[Justin Lemkul]

On 10/5/12 7:20 AM, Marlon Hinner wrote:

Please unsubscribe. Thank you.



Per the instructions in the footer of every mail on the list:

* Please don't post (un)subscribe requests to the list. Use the www interface or 
send it to gmx-users-requ...@gromacs.org.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] help with "interaction of type atom in the topology database, but an atom of that name was not found in residue" error

[Justin Lemkul]

On 8/30/12 9:23 PM, Katrina Lexa wrote:

Hello Gromacs Users:

I apologize for asking a question that has come up several times in the
forum, but I have read the answers to those posts and I am not still
unable to fix the error based on the suggestions in the previous emails.
It is completely possible that I am just not seeing the obvious, so I 
apologize,
but I would welcome any advice. I just have a methylated glycine that I 
would like to use (SAR) within a
peptide with the AMBER force field, but when I try to build the cyclic
compound it writes out:

  Opening force field file ./amber99sb_lipid.ff/atomtypes.atp
Atomtype 1
Reading residue database... (amber99sb_lipid)
Opening force field file ./amber99sb_lipid.ff/aminoacids.rtp
Residue 100
Sorting it all out...
Opening force field file ./amber99sb_lipid.ff/aminoacids.hdb
Back Off! I just backed up topol.top to ./#topol.top.59#
Processing chain 1 'A' (85 atoms, 11 residues)
Identified residue ALA1 as a starting terminus.
Identified residue ALA11 as a ending terminus.
9 out of 9 lines of specbond.dat converted successfully
Opening force field file ./amber99sb_lipid.ff/aminoacids.arn
Checking for duplicate atoms
   ---
Program pdb2gmx, VERSION 4.5.5
Source code file: pgutil.c, line: 91

Fatal error:
Atom CB is used in an interaction of type atom in the topology
database, but an atom of that name was not found in residue
number 7.

However, my residue 7 should not have a CB atom, I'm not seeing it in my
pdb file or the .rtp file (impropers section or otherwise). Perhaps that
residue is being skipped, but all of my atoms are "ATOM" rather than
HETATM, and I don't have any tabs messing up the fields.


this is the SAR (residue 7) section in my .rtp file

[ SAR ]
  [ atoms ]
  NN   -0.22670 1
 CNCT  -0.22340 2
HN1H0.10210 3
HN2H0.10210 4
HN3H0.10210 5
 CACT  -0.02520 6
HA2H1   0.06980 7
HA3H1   0.06980 8
  CC0.59730 9
  OO   -0.5679010
  [ bonds ]
  NCN
  NCA
 CA   C
 CA   HA2
 CA   HA3
 CN   HN1
 CN   HN2
 CN   HN3
  C O
 -C N
  [ impropers ]
 -CCA N H
 CA+N C O


and here is a chunk of my pdb file

MODEL1
ATOM  1  N   ALA A   1  -5.608   1.167   2.062  1.000.00
   N1+
ATOM  2  CA  ALA A   1  -4.930   0.579   3.183  1.00 0.00   
C
ATOM  3  CB  ALA A   1  -5.857   0.458   4.396  1.00 0.00   
C
ATOM  4  C   ALA A   1  -3.814   1.597   3.525  1.00 0.00   
C
ATOM  5  O   ALA A   1  -4.063   2.822   3.391  1.00  0.00  
 O
ATOM  6  N   MLE A   2  -2.575   1.132   3.819  1.00 0.00   
N
ATOM  7  CN  MLE A   2  -2.315  -0.257   4.265  1.00 0.00   
C
ATOM  8  CA  MLE A   2  -1.398   2.052   3.941  1.00 0.00   
C
ATOM  9  CB  MLE A   2  -1.091   2.218   5.462  1.00 0.00   
C
ATOM 10  CG  MLE A   2  -2.145   2.883   6.382  1.00 0.00   
C
ATOM 11  CD1 MLE A   2  -1.689   2.877   7.897  1.00 0.00   
C
ATOM 12  CD2 MLE A   2  -2.626   4.302   5.946  1.00 0.00   
C
   
   ATOM 45  N   ABA A   6 4.961   4.195  -6.289  1.00  0.00 N
ATOM 46  CA  ABA A   6 5.219   4.813  -7.615  1.00  0.00 C
ATOM 47  CB  ABA A   6 6.627   4.541  -8.037  1.00  0.00 C
ATOM 48  CG  ABA A   6 7.673   5.523  -7.418  1.00  0.00 C
ATOM 49  C   ABA A   6 4.374   4.037  -8.636  1.00  0.00 C
ATOM 50  O   ABA A   6 4.360   2.841  -8.453  1.00  0.00 O
ATOM 51  N   SAR A   7 3.818   4.705  -9.676  1.00  0.00 N
ATOM 52  CN  SAR A   7 4.087   6.071  -9.873  1.00  0.00 C
ATOM 53  CA  SAR A   7 2.929   3.969 -10.548  1.00  0.00 C
ATOM 54  C   SAR A   7 1.449   4.131 -10.258  1.00  0.00 C
ATOM 55  O   SAR A   7 0.975   5.236 -10.559  1.00  0.00 O
ATOM 56  N   MLE A   8 0.814   3.165  -9.517  1.00  0.00 N
ATOM 57  CN  MLE A   8 1.365   1.822  -9.318  1.00  0.00 C
ATOM 58  CA  MLE A   8-0.491   3.432  -8.917  1.00  0.00 C
ATOM 59  CB  MLE A   8-1.599   2.488  -9.538  1.00  0.00 C
ATOM 60  CG  MLE A   8-2.739   3.173 -10.337  1.00  0.00

Re: [gmx-users] Help of mdrun-gpu

[Mark Abraham]

On 28/07/2012 12:58 AM, Du Jiangfeng (BIOCH) wrote:

Dear All,

I just configured the mdrun-gpu.  When I tested "mdrun-gpu" by running 
gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it failed with 
segmentation fault. I don't think the system has any equilibrium problem since it works fine in 
"mdrun". I will appreciate a lot if anyone could help me for it.

Best Wishes,

Jiangfeng.



Have you read the available documentation? Do you have a supported GPU?

Mark
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Re: [gmx-users] help!!

[Justin A. Lemkul]

On 6/15/12 5:58 AM, ankita oindrila wrote:

  i am using the tutorial KALP15 in DPPC  for my protein in bilipid
membrane SIMULATION.

i have reached Step Three: Defining the Unit Cell & Adding Solvent

where i hav to pack the lipids around the protein using InflateGro.

how do i start using inflategro?

my last step was : to generate this new position restraint file using genrestr:

genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10

After which ,In the .mdp file used for the minimizations, i added  a
line "define = -DSTRONG_POSRES" to make use of these new position
restraints.

when i next gave the command :perl inflategro.pl system.gro 4 DPPC 14
system_inflated.gro 5 area.dat

ERROR  Can't open perl script "inflategro.pl": No such file or directory

WHAT SHOULD I DO???



Download the script from the link provided in the tutorial.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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RE: [gmx-users] Help with free energy

[Emanuel Birru]

Hi Milinda,

There are different methods to do Free energy. I am using Thermodynamics 
Integration method; hence if you are interested to use TI I am willing to guide 
you, but I never use bar method. I did some parametrization so if you float 
your topology and mpd files I will give you some idea how to do it.

Cheers,
Emmanuel


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Saturday, May 05, 2012 12:59 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Help with free energy

Please keep all correspondence on the gmx-users list.  I am not a private tutor
and you have better odds of solving your problem by allowing others to provide
input.

On 5/4/12 8:01 PM, Milinda Samaraweera wrote:
> Hi Justin
>
> Im a very new to using Gromacs. I tried to reproduce the values in shirts 
> paper
> for methane. And using a similar model for study the hydration of Anilinium. 
> If
> I send you my input files could you please take a look and give me some 
> suggestions.
>

Were you able to reproduce the methane hydration value?

Aniline and anilinium are different, with the latter being more difficult to
deal with on account of its charge.  If you post your topology, perhaps someone
will have some tips on how to modify it to produce better results, but proper
small molecule parameterization is not a task well-suited for new users.  It may
take considerable time and effort to derive a high-quality topology.  For
general advice, consult:

http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help with free energy

[Justin A. Lemkul]

Please keep all correspondence on the gmx-users list.  I am not a private tutor 
and you have better odds of solving your problem by allowing others to provide 
input.


On 5/4/12 8:01 PM, Milinda Samaraweera wrote:

Hi Justin

Im a very new to using Gromacs. I tried to reproduce the values in shirts paper
for methane. And using a similar model for study the hydration of Anilinium. If
I send you my input files could you please take a look and give me some 
suggestions.



Were you able to reproduce the methane hydration value?

Aniline and anilinium are different, with the latter being more difficult to 
deal with on account of its charge.  If you post your topology, perhaps someone 
will have some tips on how to modify it to produce better results, but proper 
small molecule parameterization is not a task well-suited for new users.  It may 
take considerable time and effort to derive a high-quality topology.  For 
general advice, consult:


http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help with free energy

[Justin A. Lemkul]

On 5/4/12 3:56 PM, Milinda Samaraweera wrote:

Hi

Im trying to calculate the hydration free energy for the molecule Aniline
And I get a free energy value about 10 kcal higher than the experimental value
What I do is I couple vdw then charges from a dummy state and add the two delta
G values using the g_bar method. If you have any idea why is this so
Please send me an e-mail



If the parameters do not produce observables that reflect reality (provided the 
error bars give you confidence in the value), you need a better model and thus a 
better topology.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] help about "Inconsistent DD boundary staggering limits"

[Desheng Zheng]

Thanks Justin!

about the "Software inconsistency error: Inconsistent DD boundary staggering 
limits!"

I still have three concerts.

1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5 
environmentwith the gro file and top file which were builed under Gromacs 
4.0.7 ?

2. In my protein-DPPC lipid membrane, I use the electric filed Ez is  0.3V/nm. 
whether is the value too high to induce the bowling up?

3. why do the generated  edr file in gromacs 4.5.5 environment larger than the 
edr file in gromacs 4.0.7 environment, even with the same gro file and top file 
and the same commands?

Best wishes,

Desheng





From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Thursday, April 26, 2012 3:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help about "Inconsistent DD boundary staggering
limits"

On 4/26/12 2:52 PM, Desheng Zheng wrote:
> Hi Guys,
>
> I have done the simulation. The total steps is 500. At around 90 
> steps, the error information appear like the followings.
>
> Please give me some suggestions to fix it.
>

Based on the comment that precedes the error call in the code:

/* Make sure that the grid is not shifted too much */

I would assume that this means your system has simply become unstable and is
blowing up.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

> Best wishes,
>
> Desheng
>
> --
> Program mdrun, VERSION 4.5.5
> Source code file: domdec.c, line: 3266
>
> Software inconsistency error:
> Inconsistent DD boundary staggering limits!
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)
>
>
> ---
> Program mdrun, VERSION 4.5.5
> Source code file: domdec.c, line: 3266
>
> Software inconsistency error:
> Inconsistent DD boundary staggering limits!
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)
>
> Error on node 102, will try to stop all the nodes
> Halting parallel program mdrun on CPU 102 out of 120
> Error on node 105, will try to stop all the nodes
> Halting parallel program mdrun on CPU 105 out of 120
> Error on node 51, will try to stop all the nodes
> Halting parallel program mdrun on CPU 51 out of 120
>
> ---
> Program mdrun, VERSION 4.5.5
> Source code file: domdec.c, line: 3266
>
> Software inconsistency error:
> Inconsistent DD boundary staggering limits!
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)
>
> Error on node 81, will try to stop all the nodes
> Halting parallel program mdrun on CPU 81 out of 120
>
> ---
> Program mdrun, VERSION 4.5.5
> Source code file: domdec.c, line: 3266
>
> Software inconsistency error:
> Inconsistent DD boundary staggering limits!
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)
>
> Error on node 63, will try to stop all the nodes
> Halting parallel program mdrun on CPU 63 out of 120
>
> ---
> Program mdrun, VERSION 4.5.5
> Source code file: domdec.c, line: 3266
>
> Software inconsistency error:
> Inconsistent DD boundary staggering limits!
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "If it weren't for bad luck, we'd have no luck at all" (The Unthanks)
>
> Error on node 33, will try to stop all the nodes
> Halting parallel program mdrun on CPU 33 out of 120
>
> ---

Re: [gmx-users] help about "Inconsistent DD boundary staggering limits"

[Justin A. Lemkul]

On 4/26/12 3:30 PM, Desheng Zheng wrote:

Thanks Justin!

about the "Software inconsistency error: Inconsistent DD boundary staggering
limits!"

I still have three concerts.

1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5
environmentwith the gro file and top file which were builed under Gromacs
4.0.7 ?



Coordinate files and topologies are largely independent of version.  There was a 
reorganization of the force fields between 4.0.7 and 4.5, but you can easily 
work around such things.



2. In my protein-DPPC lipid membrane, I use the electric filed Ez is
0.3V/nm. whether is the value too high to induce the bowling up?



I don't know.  The easiest way to deduce the source of the problem is to do so 
scientifically.  Turn off the electric field, does the simulation run? 
Eliminate other factors systematically until you arrive at the root of the problem.



3. why do the generated  edr file in gromacs 4.5.5 environment larger than
the edr file in gromacs 4.0.7 environment, even with the same gro file and
top file and the same commands?



There have been changes to the .edr format and its contents to allow for more 
features.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Please search the archive at 
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Re: [gmx-users] help about "Inconsistent DD boundary staggering limits"

[Justin A. Lemkul]

On 4/26/12 2:52 PM, Desheng Zheng wrote:

Hi Guys,

I have done the simulation. The total steps is 500. At around 90 steps, 
the error information appear like the followings.

Please give me some suggestions to fix it.



Based on the comment that precedes the error call in the code:

/* Make sure that the grid is not shifted too much */

I would assume that this means your system has simply become unstable and is 
blowing up.


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin


Best wishes,

Desheng

--
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


---
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 102, will try to stop all the nodes
Halting parallel program mdrun on CPU 102 out of 120
Error on node 105, will try to stop all the nodes
Halting parallel program mdrun on CPU 105 out of 120
Error on node 51, will try to stop all the nodes
Halting parallel program mdrun on CPU 51 out of 120

---
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 81, will try to stop all the nodes
Halting parallel program mdrun on CPU 81 out of 120

---
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 63, will try to stop all the nodes
Halting parallel program mdrun on CPU 63 out of 120

---
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 33, will try to stop all the nodes
Halting parallel program mdrun on CPU 33 out of 120

---
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)


---
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"If it weren't for bad luck, we'd have no luck at all" (The Unthanks)

Error on node 54, will try to stop all the nodes
Halting parallel program mdrun on CPU 54 out of 120
Error on node 24, will try to stop all the nodes
Halting parallel program mdrun on CPU 24 out of 120

---
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"If it weren't for bad luck, we'd have no luck at 

Re: [gmx-users] Help: Anyone worked with "Wall"?

[Peter C. Lai]

For walls, the atoms in the wall are virtual. 
Remember that 9-3 LJ integratees over the volume behind the wall so you will
have to set your atom density appropriately. Setting wall_density to 20/nm^3
for 9-3 wall leads to 20 carbon atoms per nm^3. That's not going to be 
totally solid, imo.

I am using 10-4 "2-D" walls to effect here:
nwall = 2
wall_type = 10-4
wall_density = 5 5
wall_atomtype = CG331 CG331
wall_r_linpot = -1
wall_ewald_zfac = 3
ewald_geometry=3dc
pbc=xy

(CG331 is just a methyl group carbon specific to my forcefield).


On 2012-04-05 10:08:02PM +0200, Huaichen(Bobby) Zhang wrote:
> Dear all,
> 
> I'm trying to simulate with pbc=xy and I need two walls. My settings are as
> follows:
> 
> pbc =  xy
> nwall   =  2
> wall_atomtype   =  C C
> wall_type   =  9-3
> wall_r_linpot   =  -1 -1
> wall_density=  20 20
> wall_ewald_zfac =  3
> 
> The problem is how to define wall_atomtype in my topology file (top/itp)? A
> want to have this solid carbon wall with 9-3 potential. Where in my top/itp
> file can I define such atoms? This is my top file:
> 
> #include "ffG53a6.itp"
> #include "spc.itp"
> 
> [ system ]
> Pure Water with walls
> 
> [ molecules ]
> SOL216
> 
> When I gmxdump the generated tpr file, I saw no C atoms are defined; and it
> showed:
> 
>wall_atomtype[0] = 2
>wall_atomtype[1] = 2
> 
> which corresponds to the hydrogen atom in my top file. And according to my
> forcefield, the LJ parameters for H is 0,0. So there is basically no wall.
> When I tried to simulate with this setting, the water molecules went out of
> the box (in z direction) and moved far away. And according to g_energy,
> there is no interaction energy between water and wall. So there indeed is
> no wall.
> 
> Can you help me with defining wall atom? If you have already finished any
> tasks with this wall algorithm, can you kindly attach your topology files
> to me?
> 
> Soo many thanks!
> 
> 
> -- 
> Huaichen(Bobby) ZHANG
> 
> +31 648478172
> MSc Sustainable Energy Engineering
> Royal Institute of Technology (Sweden)
> Eindhoven University of Technology (Netherland)

> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] help needed

[Mark Abraham]

On 31/03/2012 6:02 PM, oindrila das wrote:

*SIMULATION OF LYSOZYME IN WATER USING GROMACS-4.0.5
*
STEP: TO NEUTRALIZE THE +8 CHARGE WITH 8 CL- MOLECULES*


COMMAND GIVEN :

[root@localhost gromacs-4.0.5]# genion -s ions.tpr -o 
1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8*

 :-)  G  R  O  M  A  C  S  (-:

   GRoups of Organic Molecules in ACtion for Science

:-)  VERSION 4.0.5  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org  
for more information.


 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  genion  (-:

Option Filename  Type Description

  -s   ions.tpr  InputRun input file: tpr tpb tpa
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
  -n  index.ndx  Input, Opt.  Index file
  -o 1AKI_solv_ions.gro  Output   Structure file: gro g96 pdb
  -g genion.log  Output   Log file
-potpot.pdb  Output, Opt. Protein data bank file
  -p  topol.top  In/Out, Opt! Topology file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint19  Set the nicelevel
-[no]xvgrbool   yes Add specific codes (legends etc.) in the 
output

xvg files for the xmgrace program
-np  int0   Number of positive ions
-pname   string NA  Name of the positive ion
-pq  int1   Charge of the positive ion
-nn  int8   Number of negative ions
-nname   string CL  Name of the negative ion
-nq  int-1  Charge of the negative ion
-rminreal   0.6 Minimum distance between ions
-[no]random  bool   yes Use random placement of ions instead of 
based on

potential. The rmin option should still work
-seedint1993Seed for random number generator
-scale   real   0.001   Scaling factor for the potential for -pot
-concreal   0   Specify salt concentration (mol/liter). 
This will
add sufficient ions to reach up to the 
specified
concentration as computed from the volume 
of the
cell in the input tpr file. Overrides the 
-np and

nn options.
-[no]neutral bool   no  This option will add enough ions to neutralize
the system. In combination with the 
concentration

option a neutral system at a given salt
concentration will be generated.

WARNING: turning of free energy, will use lambda=0
Reading file ions.tpr, VERSION 4.0.5 (single precision)
Using a coulomb cut-off of 1 nm
Will try to add 0 NA ions and 8 CL ions.
Select a continuous group of solvent molecules
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group 0 (  System) has 39055 elements
Group 1 ( Protein) has  1960 elements
Group 2 (   Protein-H) has  1001 elements
Group 3 ( C-alpha) has   129 elements
Group 4 (Backbone) has   387 elements
Group 5 (   MainChain) has   517 elements
Group 6 (MainChain+Cb) has   634 elements
Group 7 ( MainChain+H) has   646 elements
Group 8 (   SideChain) has  1314 elements
Group 9 ( SideChain-H) has   484 elements
Group10 ( Prot-Masses) has  1960 elements
Group11 ( Non-Protein) has 37095 elements
Group12 ( SOL) has 37095 elements
Group13 (   Other) has 37095 elements
Select a group: 12
Selected 12: 'SOL'
Number of (3-atomic) solvent molecules: 12365

Processing topology
Replacing 12357 solute molecules in topology file (topol.top)  by 0 NA 
and 8 CL ions.


Back Off! I just backed up topol.top to ./#topol.top.2#
Replacing solvent molecule 1450 (atom 6310) with CL
Replacing solvent molecule 9368 (atom 30064) with CL
Replacing solvent molecule 6035 (atom 20065) with CL
Replacing solvent molecule 10461 (atom 33343) with CL
Replacing solvent molecule 4117 (atom 14311) with CL
Replacing solvent molecule 1980 (atom 7900) with CL
Replacing solvent molecule 4774 (atom 16282) with CL
Replacing solvent molecule 10956 (atom 34828) with CL

_THE PROBLEM FACED IS_:
THE REPLACED CL MOLECULES CANNOT BE SEEN IN THE UPDATED TOPOLOGY FILE. 
PLEASE TELL ME HOW TO ANALYSE IT.


What do you mean by "can

Re: [gmx-users] Help regarding running DSSP in gmx

[Mark Abraham]

On 20/03/2012 12:39 AM, chandran karunakaran wrote:

Dear ALL,

We could not run DSSP for analysing the secondary structure. 
Any help in this regard is very much appreciated


***+
Dr.Karunakaran Chandran +
Biophysics Department +
Medical College of Wisconsin +
Milwaukee, WI-53226 +
Resi.: 414-443-0085 +
Off : 414-456-4034 +


You're doing something wrong :-) Please consider and follow the advice 
here http://www.gromacs.org/Support and ask again.


Mark
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Re: [gmx-users] Help regarding running DSSP in gmx

[Tsjerk Wassenaar]

Hi Chandran,

What did you try, and what error did it come up with? What platform
are you using, and which version of DSSP? The latest version of DSSP
won't work with Gromacs yet.

Cheers,

Tsjerk


On Mon, Mar 19, 2012 at 2:39 PM, chandran karunakaran
 wrote:
> Dear ALL,
>
>     We could not run DSSP for analysing the secondary structure. Any
> help in this regard is very much appreciated
>
>
> ***+
> Dr.Karunakaran Chandran +
> Biophysics Department +
> Medical College of Wisconsin +
> Milwaukee, WI-53226 +
> Resi.: 414-443-0085 +
> Off : 414-456-4034 +
> 
> 
> From: "gmx-users-requ...@gromacs.org" 
> To: gmx-users@gromacs.org
> Sent: Monday, 19 March 2012 4:30 PM
> Subject: gmx-users Digest, Vol 95, Issue 125
>
> Send gmx-users mailing list submissions to
>     gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>     gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
>     gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>   1. Editing potential parameters (Asaf Farhi)
>   2. nrexcl in topology (Lara Bunte)
>   3. extending simulation (priya thiyagarajan)
>   4. Re: nrexcl in topology (R.Perez Garcia)
>   5. Re: Force constant - Umbrella Sampling (lloyd riggs)
>
>
> --
>
> Message: 1
> Date: Mon, 19 Mar 2012 10:06:47 +
> From: Asaf Farhi 
> Subject: [gmx-users] Editing potential parameters
> To: "gmx-users@gromacs.org" 
> Message-ID: <7D02BCA1E8377E4AABC2E8F59B6D0CDA09E25B@IBWMBX01>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Gromacs user
>
> Hi. My name is Asaf and I'm trying to edit potential parameters for the non
> bonded interaction potential terms between specific atoms (k1 for 1 subset
> of pairs and k2 for anoother subset of pairs).
> Is the pairs section in the topology file the correct place to do this? and
> if so how would you incorporate spring constant for particular pair
> interaction?
>
> Many thanks.
> Best regards,
> Asaf
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/6adac179/attachment-0001.html
>
> --
>
> Message: 2
> Date: Mon, 19 Mar 2012 10:19:22 + (GMT)
> From: Lara Bunte 
> Subject: [gmx-users] nrexcl in topology
> To: "gmx-users@gromacs.org" 
> Message-ID:
>     <1332152362.73030.yahoomail...@web29401.mail.ird.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi
>
> in a topology file in the section [ moleculetypes ] is standing
>
> ; nrexcl
>
>     3
>
> What do this mean?
>
> Thanks for help
> Greetings
> Lara
>
>
> --
>
> Message: 3
> Date: Mon, 19 Mar 2012 03:26:55 -0700
> From: priya thiyagarajan 
> Subject: [gmx-users] extending simulation
> To: gmx-users@gromacs.org
> Message-ID:
>     
> Content-Type: text/plain; charset="iso-8859-1"
>
> hello sir,,
>
> initially i did my simulation for 10ns.. after getting result i analysed it
> and thought of extending the simulation for another 10ns..
>
> i used following commands..
>
> tpbconv *-s md.tpr -o newmd.tpr -extend 1.00*
>
> *mdrun -s newmd.tpr -o md3_2.trr -c md_2.gro -e md_2.edr -g md_2.log -cpi
> state1.cpt -noappend*
>
>
> is it correct..
>
> we ll use tpbconv to extend the simulation which terminated in the middle..
>
> is it correct to use the same command for completed run...
>
> please help me with your answer..
>
> Thanking you sir,
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/9248f3aa/attachment-0001.html
>
> --
>
> Message: 4
> Date: Mon, 19 Mar 2012 11:27:43 +0100
> From: "R.Perez Garcia" 
> Subject: Re: [gmx-users] nrexcl in topology
> To: Lara Bunte , "gmx-users@gromacs.org"
>     
> Message-ID: <7630868d774ff.4f671...@rug.nl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-May/061072.html
>
> On 19-03-12, Lara Bunte   wrote:
>> Hi
>>
>> in a topology file in the section [ moleculetypes ] is standing
>>
>> ; nrexcl
>>
>>     3
>>
>> What do this mean?
>>
>> Thanks for help
>> Greetings
>> Lara
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.groma

Re: [gmx-users] help on replica exchange dynamics with gromacs

[Mark Abraham]

On 13/03/2012 3:17 PM, Raghuvir Pissurlenkar wrote:

Dear friends

Can someone help me with tutorial on replica exchange dynamics


Thanks in advance

Raghuvir




Search the GROMACS webpage, please. You will want to do some normal 
tutorials to understand normal workflows first.


Mark
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Re: [gmx-users] Help about g_hbond and angle cutoff

[Justin A. Lemkul]

alejandro esteban blanco munoz wrote:

Hi gromacs Users:

I have a doubt respect to how g_hbond consider the cutoff angle (-a) 
Acceptor-Donnor-Hydrogen in gromacs 4.5.4. I need to evaluate the 
hydrogen bonds with an anble larger than 135°. The default value of the 
angle is cutoff in g_hbond is 30°, so this value means that the H. bonds 
larger than 30° will be evaluated? or the angles to evaluate will be 
larger than 150° (180° - 30°) as is proposed in this post for gromacs 
3.1.1: http://lists.gromacs.org/pipermail/gmx-users/2003-January/003970.html
If the second case was correct, then the value to use in my case  should 
be "-a 45" for looking all H. bonds larger than 135°?




Yes, note the order of the terms.  The default value of 30 degrees corresponds 
to the A-D-H angle, so that would make the D-H-A value (which is I think what 
you are considering) 150 degrees in the default case.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help with non-standard residues and molecular structures

[Robert Hamers]

Thanks-- that clarifies a lot.  I hadn't quite realized how much is 
assumed about the residue terminii.  It seems like I was trying to fit a 
square peg into a round hole.   I'm going to re-think this and maybe 
take a different approach just based on using HETATMs and not trying to 
define a separate residue.


The pdb file specification for HETATM still requires a "residue name".  
I've found that using "LIG" seems to work. Any reason I shouldn't just 
continue using that, and define my molecule using HETATMs ?


Thanks again for your help!
Bob Hamers

For something like what I'm trying to do, where I"m using a pdb file 
that does not represent a protein, is


On 1/4/2012 2:02 AM, Mark Abraham wrote:

On 4/01/2012 4:57 PM, Robert Hamers wrote:

I'd appreciate any help  --

I'm trying to model a small (~ 20-carbon ) molecule linked to a 
diamond surface.  I got the diamond surface with >1500 atoms working 
fine all the way through to the MD simulation and it looks great.  
But I'm getting stuck on the molecule, which is not a protein but a 
moderately short-chain molecule that has a triazole (N3C2) in the 
middle of it.  I thought in order to make this work I would need ot 
learn how to with non-standard residues and after reading through the 
manual endless times and searching on the web site and trying things 
I'm basically stuck.


I thought it would easiest to deal with the triazole ring by creating 
it as a non-standard residue in aminoacids.n2t.  As a starting point 
I thought I would try to work slowly by modifying an existing 
residue, so I arbitrary decided to modify "alanine" in order to 
understand how to work toward the more complicated triazole ring.  
So, in atomtypebyname.atp I copied the entry for ALA and called it 
ZZZ, and added a new entry "ZZZ  Protein" into "residuetypes.dat".  
At that point I can read in a pdb file with atoms belonging to 
residue "ZZZ" and pdb2gmx works fine.  However,  if I try to change 
one of the carbon atoms
to a nitrogen, (say, chance CA to N or NA), I get errors (see below) 
that I'm having trouble interpreting.  I thought that perhaps it was 
a problem of having two atoms with the same definition, so I made one 
"N1" and one "N2" as below, and also tried other variations (e.g., 
NA1 and NA2)


Atom naming needs to be unique within the residue, so that grompp can 
later confirm that the order of the names in the topology and 
coordinate files match.




(This is my entry in aminoacids.n2t)


aminoacids.rtp I assume you mean.


[ ZZZ ]
 [ atoms ]
N1opls_238   -0.500 1
 Hopls_2410.300 1
N2   opls_238  0.140 1
HAopls_1400.060 1
CBopls_135   -0.180 2
   HB1opls_1400.060 2
   HB2opls_1400.060 2
   HB3opls_1400.060 2
 Copls_2350.500 3
 Oopls_236   -0.500 3
 [ bonds ]
 N1 H
 N1N2
N2HA
N2CB
N2 C
CB   HB1
CB   HB2
CB   HB3
 C O
-C N1
 [ impropers ]
-CN2 N1 Himproper_Z_N_X_Y
N2+N1 C Oimproper_O_C_X_Y

I thought that this would lead to a structure that would connect "C" 
to the previous residue in my pdb file and the "N" to the next . 
However, when I do pdb2gmx, I get:


*N2* to the next, but yeah...


**
Back Off! I just backed up topol.top to ./#topol.top.40#
Processing chain 1 (13 atoms, 1 residues)
There are 0 donors and 1 acceptors
There are 0 hydrogen bonds
Identified residue ZZZ1 as a starting terminus.
Identified residue ZZZ1 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ZZZ-1: NH3+
End terminus ZZZ-1: COO-


So the default(?) terminus selection is trying to give you charged 
termini (perhaps because the type is protein, but I'm not sure here). 
It is always appropriate to supply the command line you used.




---
Program pdb2gmx, VERSION 4.5.3
Source code file: /build/buildd/gromacs-4.5.3/src/kernel/pdb2top.c, 
line: 1056


Fatal error:
atom N not found in buiding block 1ZZZ while combining tdb and rtp


aminoacids.n.tdb applies to protein residues and assumes that NH3+ can 
be applied. Evidently that won't work for your case. You will need to 
come up with some termini that make sense, or use more than one residue.





I'm using the oplsaa force field, but up to this point it was a 
pretty arbitrary decision.
I think my problem is understanding the mapping between atom names ( 
N1, HB1, etc) and the opls names, as I haven't yet found a good 
explanation for how this mapping is done and/or what flexibility one 
has in creating atom names for non-standard residues.  (So, am I 
allowed to create a N atom and call it N1, as long as I assign it to 
an existing opls_xxx number ?) .


Yes. Atom and residue names exist only for matching pieces of force 
fields together. The atom type determines the physics of the result

Re: [gmx-users] Help with non-standard residues and molecular structures

[Mark Abraham]

On 4/01/2012 4:57 PM, Robert Hamers wrote:

I'd appreciate any help  --

I'm trying to model a small (~ 20-carbon ) molecule linked to a 
diamond surface.  I got the diamond surface with >1500 atoms working 
fine all the way through to the MD simulation and it looks great.  But 
I'm getting stuck on the molecule, which is not a protein but a 
moderately short-chain molecule that has a triazole (N3C2) in the 
middle of it.  I thought in order to make this work I would need ot 
learn how to with non-standard residues and after reading through the 
manual endless times and searching on the web site and trying things 
I'm basically stuck.


I thought it would easiest to deal with the triazole ring by creating 
it as a non-standard residue in aminoacids.n2t.  As a starting point I 
thought I would try to work slowly by modifying an existing residue, 
so I arbitrary decided to modify "alanine" in order to understand how 
to work toward the more complicated triazole ring.  So, in 
atomtypebyname.atp I copied the entry for ALA and called it ZZZ, and 
added a new entry "ZZZ  Protein" into "residuetypes.dat".  At that 
point I can read in a pdb file with atoms belonging to residue "ZZZ" 
and pdb2gmx works fine.  However,  if I try to change one of the 
carbon atoms
to a nitrogen, (say, chance CA to N or NA), I get errors (see below) 
that I'm having trouble interpreting.  I thought that perhaps it was a 
problem of having two atoms with the same definition, so I made one 
"N1" and one "N2" as below, and also tried other variations (e.g., NA1 
and NA2)


Atom naming needs to be unique within the residue, so that grompp can 
later confirm that the order of the names in the topology and coordinate 
files match.




(This is my entry in aminoacids.n2t)


aminoacids.rtp I assume you mean.


[ ZZZ ]
 [ atoms ]
N1opls_238   -0.500 1
 Hopls_2410.300 1
N2   opls_238  0.140 1
HAopls_1400.060 1
CBopls_135   -0.180 2
   HB1opls_1400.060 2
   HB2opls_1400.060 2
   HB3opls_1400.060 2
 Copls_2350.500 3
 Oopls_236   -0.500 3
 [ bonds ]
 N1 H
 N1N2
N2HA
N2CB
N2 C
CB   HB1
CB   HB2
CB   HB3
 C O
-C N1
 [ impropers ]
-CN2 N1 Himproper_Z_N_X_Y
N2+N1 C Oimproper_O_C_X_Y

I thought that this would lead to a structure that would connect "C" 
to the previous residue in my pdb file and the "N" to the next . 
However, when I do pdb2gmx, I get:


*N2* to the next, but yeah...


**
Back Off! I just backed up topol.top to ./#topol.top.40#
Processing chain 1 (13 atoms, 1 residues)
There are 0 donors and 1 acceptors
There are 0 hydrogen bonds
Identified residue ZZZ1 as a starting terminus.
Identified residue ZZZ1 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ZZZ-1: NH3+
End terminus ZZZ-1: COO-


So the default(?) terminus selection is trying to give you charged 
termini (perhaps because the type is protein, but I'm not sure here). It 
is always appropriate to supply the command line you used.




---
Program pdb2gmx, VERSION 4.5.3
Source code file: /build/buildd/gromacs-4.5.3/src/kernel/pdb2top.c, 
line: 1056


Fatal error:
atom N not found in buiding block 1ZZZ while combining tdb and rtp


aminoacids.n.tdb applies to protein residues and assumes that NH3+ can 
be applied. Evidently that won't work for your case. You will need to 
come up with some termini that make sense, or use more than one residue.





I'm using the oplsaa force field, but up to this point it was a pretty 
arbitrary decision.
I think my problem is understanding the mapping between atom names ( 
N1, HB1, etc) and the opls names, as I haven't yet found a good 
explanation for how this mapping is done and/or what flexibility one 
has in creating atom names for non-standard residues.  (So, am I 
allowed to create a N atom and call it N1, as long as I assign it to 
an existing opls_xxx number ?) .


Yes. Atom and residue names exist only for matching pieces of force 
fields together. The atom type determines the physics of the resulting 
model. The two are technically orthogonal, but in practice there are 
strong correlations.


Mark
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Re: [gmx-users] Help with Principal component analysis

[Mark Abraham]

On 3/01/2012 6:54 AM, Alex Jemulin wrote:

Dear all
I run a MD on a GPCR (transmembrane protein)
Then I run a PCA on results and I found 3PC sufficient to explain 
variance.
On the same PC I get big values for samples located both at Nter 
(extracellular) and Cter (intracellular) or for similar cases such as 
both Nter(extracellular) and Loop5 (intracellular).According to you 
how could I explain the motion of group atoms intra and extracellular 
on the same components?
Does it mean the motion of some atoms at Nter (for instance) could 
influence the motion at Cter ? Could it be logic?


Highly unlikely. You don't give any details of your simulation, so your 
simulation could be too short, or have insufficient distance between 
your periodic images.


Mark
-- 
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RE: [gmx-users] Help with g_density

[Dallas Warren]

What is your interpretation?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Alex Jemulin
Sent: Tuesday, 20 December 2011 7:57 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Help with g_density

Dear All
I run g_density on a membrane protein.
Here are the results

http://elisacarli.altervista.org/densityhead.jpg
http://elisacarli.altervista.org/tailsDensity.jpg

Could you help me to give an interpretation to my analysis?

Thank in advance
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Re: [gmx-users] Help with g_rmsf

[Tsjerk Wassenaar]

Hi Carla,

> during my simulation, the dimer I'm simulating changed a lot.
> So when I calculate with g_rms, the RMSD between my initial and my final
> structure (choosing "Protein-H"), I get a value of 10 angstroms.

Have you made sure there are no atoms jumping across the boundaries?

> g_rmsf -s initial.pdb -f final.pdb -od rmsdev.xvg -res (I choose
> "chainA-H"),

If you choose chainA-H, you'll get results for that chain. It will be
used for the fit as well as for the analysis.

> does g_rmsf fit one the whole dimer and then calculate rmsdeviation of
> chainA or does it fit on chainA and then calculate RMSdeviation of chainA.
> In the latter case, my result does not reflect the reality of my simulation.

It does reflect the reality of your simulation. Maybe it does not
reflect what you aimed to get.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] help on mdrun

[lina]

I am not sure I can give an affirmative working answer, but you may check

ssh to each node, use "top" to see whether it's really run or just
occupy the node but not use.



On Sat, Jul 9, 2011 at 8:56 AM, Mark Abraham  wrote:
> On 9/07/2011 3:37 AM, raghu...@bcpindia.org wrote:
>>
>> Hi
>>
>>
>> I have a problem related to submitting a mdrun job on cluster.  I tried to
>> ask help or gromacs and rocks users-group.
>>
>> My machine specs.
>> Cluster of Intel Xeon processors:QC with Rocks Cluster.  8 processors (16
>> threads)
>>
>> When I submit mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px
>> pullx-umbrella0.xvg on the localhost, the job takes note of 16 threads and
>> the job completes in a day.  But when I try submitting it to the cluster
>> using following qsub script the job takes ~16 days
>>
>> ---
>> #!/bin/bash
>> #
>> #$ -cwd
>> #$ -S /bin/bash
>> #
>> #$ -N umbrella0
>> #$ -e umbrella0.errout
>> #$ -o umbrella0.out
>> #
>> #$ -pe mpi 16
>>
>> echo -n "Running on: "
>>
>> /opt/openmpi/bin/mpirun -np 16 -machinefile /home/raghuvir/machines
>> /share/apps/gromacs-4.5.3/bin/mdrunmpi -deffnm umbrella0 -pf
>> pullf-umbrella0.xvg -px pullx-umbrella0.xvg
>>
>> echo "Done."
>> ---
>
> That's fine as far as GROMACS is concerned, so long as mdrunmpi really has
> been compiled with MPI. You can get what diagnostic information it knows
> about the MPI setup from the very top of the .log file. Otherwise, you'll
> have troubleshoot your use of MPI and your batch queue system.
>
> Mark
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-- 
Best Regards,

lina
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Re: [gmx-users] help on mdrun

[Mark Abraham]

On 9/07/2011 3:37 AM, raghu...@bcpindia.org wrote:

Hi


I have a problem related to submitting a mdrun job on cluster.  I 
tried to ask help or gromacs and rocks users-group.


My machine specs.
Cluster of Intel Xeon processors:QC with Rocks Cluster.  8 processors 
(16 threads)


When I submit mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px 
pullx-umbrella0.xvg on the localhost, the job takes note of 16 threads 
and the job completes in a day.  But when I try submitting it to the 
cluster using following qsub script the job takes ~16 days


---
#!/bin/bash
#
#$ -cwd
#$ -S /bin/bash
#
#$ -N umbrella0
#$ -e umbrella0.errout
#$ -o umbrella0.out
#
#$ -pe mpi 16

echo -n "Running on: "

/opt/openmpi/bin/mpirun -np 16 -machinefile /home/raghuvir/machines 
/share/apps/gromacs-4.5.3/bin/mdrunmpi -deffnm umbrella0 -pf 
pullf-umbrella0.xvg -px pullx-umbrella0.xvg


echo "Done."
---


That's fine as far as GROMACS is concerned, so long as mdrunmpi really 
has been compiled with MPI. You can get what diagnostic information it 
knows about the MPI setup from the very top of the .log file. Otherwise, 
you'll have troubleshoot your use of MPI and your batch queue system.


Mark
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Re: [gmx-users] help

[Mark Abraham]

On 8/07/2011 1:31 PM,  wrote:

Hi,
I'm doing implicit solvent in gromacs 4.5.2 with amber03 force field 
.I have done energy minimization .Then mdrun in NVT,but there is 
always LINCS error .When I make impolicit_solvent=no,it can run 
successfully. Is there a problem in the parameter settings? How can I 
solve the problem?

Step 49, time 0.049 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 56.816425, max 1019.791504 (between atoms 2943 and 2942)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2913 2912 90.1 0.1093 62.1434 0.1093
2920 2919 91.3 0.1093 4.7180 0.1093
2943 2942 90.1 0.1895 99.4251 0.0974
Wrote pdb files with previous and current coordinates
mdp file is in the attachment.




There's a few threads like this in the archives. Probably a smaller time 
step while equilibrating is in order.


Mark
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Re: [gmx-users] Help: Gromacs Installation

[Mark Abraham]

On 4/28/2011 4:44 AM, Hrachya Astsatryan wrote:

Dear Roland,

We need to run the GROMACS on the base of the nodes of our cluster (in 
order to use all computational resources of the cluster), that's why 
we need MPI (instead of using thread or OpenMP within the SMP node).
I can run simple MPI examples, so I guess the problem on the 
implementation of the Gromacs.


I agree with Roland that the problem is likely to be in the 
configuration and function of the MPI library. RHEL4, being at least 5 
years old, is probably using some ancient MPI library version that is 
not up to the job. This is frequently-occurring problem. Roland asked 
about your MPI library... if you want free help, you'll do yourself 
favours by providing answers to the questions of people who are offering 
help :-)


Mark


On 4/27/11 11:29 PM, Roland Schulz wrote:
This seems to be a problem with your MPI library. Test to see whether 
other MPI programs don't have the same problem. If it is not GROMACS 
specific please ask on the mailinglist of your MPI library. If it 
only happens with GROMACS be more specific about what your setup is 
(what MPI library, what hardware, ...).


Also you could use the latest GROMACS 4.5.x. It has built in thread 
support and doesn't need MPI as long as you only run on n cores 
within one SMP node.


Roland

On Wed, Apr 27, 2011 at 2:13 PM, Hrachya Astsatryan > wrote:


Dear Mark Abraham & all,

We  used another benchmarking systems, such as d.dppc on 4
processors, but we have the same problem (1 proc use about 100%,
the others 0%).
After for a while we receive the following error:

Working directory is /localuser/armen/d.dppc
Running on host wn1.ysu-cluster.grid.am

Time is Fri Apr 22 13:55:47 AMST 2011
Directory is /localuser/armen/d.dppc
START
Start: Fri Apr 22 13:55:47 AMST 2011
p2_487:  p4_error: Timeout in establishing connection to remote
process: 0
rm_l_2_500: (301.160156) net_send: could not write to fd=5, errno
= 32
p2_487: (301.160156) net_send: could not write to fd=5, errno = 32
p0_32738:  p4_error: net_recv read:  probable EOF on socket: 1
p3_490: (301.160156) net_send: could not write to fd=6, errno = 104
p3_490:  p4_error: net_send write: -1
p3_490: (305.167969) net_send: could not write to fd=5, errno = 32
p0_32738: (305.371094) net_send: could not write to fd=4, errno = 32
p1_483:  p4_error: net_recv read:  probable EOF on socket: 1
rm_l_1_499: (305.167969) net_send: could not write to fd=5, errno
= 32
p1_483: (311.171875) net_send: could not write to fd=5, errno = 32
Fri Apr 22 14:00:59 AMST 2011
End: Fri Apr 22 14:00:59 AMST 2011
END

We tried new version of Gromacs, but receive the same error.
Please, help us to overcome the problem.


With regards,
Hrach


On 4/22/11 1:41 PM, Mark Abraham wrote:

On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote:

Dear all,

I would like to inform you that I have installed the
gromacs4.0.7 package on the cluster (nodes of the cluster
are 8 core Intel, OS: RHEL4 Scientific Linux) with the
following steps:

yum install fftw3 fftw3-devel
./configure --prefix=/localuser/armen/gromacs --enable-mpi

Also I have downloaded gmxbench-3.0 package and try to
run d.villin to test it.

Unfortunately it wok fine until np is 1,2,3, if I use
more than 3 procs I receive low CPU balancing and the
process in hanging.

Could you, please, help me to overcome the problem?


Probably you have only four physical cores (hyperthreading is
not normally useful), or your MPI is configured to use only
four cores, or these benchmarks are too small to scale usefully.

Choosing to do a new installation of a GROMACS version that
is several years old is normally less productive than the
latest version.

Mark




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865-241-1537, ORNL PO BOX 2008 MS6309







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Re: [gmx-users] Help: Gromacs Installation

[Hrachya Astsatryan]

Dear Roland,

We need to run the GROMACS on the base of the nodes of our cluster (in 
order to use all computational resources of the cluster), that's why we 
need MPI (instead of using thread or OpenMP within the SMP node).
I can run simple MPI examples, so I guess the problem on the 
implementation of the Gromacs.



Regads,
Hrach

On 4/27/11 11:29 PM, Roland Schulz wrote:
This seems to be a problem with your MPI library. Test to see whether 
other MPI programs don't have the same problem. If it is not GROMACS 
specific please ask on the mailinglist of your MPI library. If it only 
happens with GROMACS be more specific about what your setup is (what 
MPI library, what hardware, ...).


Also you could use the latest GROMACS 4.5.x. It has built in thread 
support and doesn't need MPI as long as you only run on n cores within 
one SMP node.


Roland

On Wed, Apr 27, 2011 at 2:13 PM, Hrachya Astsatryan > wrote:


Dear Mark Abraham & all,

We  used another benchmarking systems, such as d.dppc on 4
processors, but we have the same problem (1 proc use about 100%,
the others 0%).
After for a while we receive the following error:

Working directory is /localuser/armen/d.dppc
Running on host wn1.ysu-cluster.grid.am

Time is Fri Apr 22 13:55:47 AMST 2011
Directory is /localuser/armen/d.dppc
START
Start: Fri Apr 22 13:55:47 AMST 2011
p2_487:  p4_error: Timeout in establishing connection to remote
process: 0
rm_l_2_500: (301.160156) net_send: could not write to fd=5, errno = 32
p2_487: (301.160156) net_send: could not write to fd=5, errno = 32
p0_32738:  p4_error: net_recv read:  probable EOF on socket: 1
p3_490: (301.160156) net_send: could not write to fd=6, errno = 104
p3_490:  p4_error: net_send write: -1
p3_490: (305.167969) net_send: could not write to fd=5, errno = 32
p0_32738: (305.371094) net_send: could not write to fd=4, errno = 32
p1_483:  p4_error: net_recv read:  probable EOF on socket: 1
rm_l_1_499: (305.167969) net_send: could not write to fd=5, errno = 32
p1_483: (311.171875) net_send: could not write to fd=5, errno = 32
Fri Apr 22 14:00:59 AMST 2011
End: Fri Apr 22 14:00:59 AMST 2011
END

We tried new version of Gromacs, but receive the same error.
Please, help us to overcome the problem.


With regards,
Hrach


On 4/22/11 1:41 PM, Mark Abraham wrote:

On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote:

Dear all,

I would like to inform you that I have installed the
gromacs4.0.7 package on the cluster (nodes of the cluster
are 8 core Intel, OS: RHEL4 Scientific Linux) with the
following steps:

yum install fftw3 fftw3-devel
./configure --prefix=/localuser/armen/gromacs --enable-mpi

Also I have downloaded gmxbench-3.0 package and try to run
d.villin to test it.

Unfortunately it wok fine until np is 1,2,3, if I use more
than 3 procs I receive low CPU balancing and the process
in hanging.

Could you, please, help me to overcome the problem?


Probably you have only four physical cores (hyperthreading is
not normally useful), or your MPI is configured to use only
four cores, or these benchmarks are too small to scale usefully.

Choosing to do a new installation of a GROMACS version that is
several years old is normally less productive than the latest
version.

Mark




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865-241-1537, ORNL PO BOX 2008 MS6309


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Re: [gmx-users] Help: Gromacs Installation

[Roland Schulz]

This seems to be a problem with your MPI library. Test to see whether other
MPI programs don't have the same problem. If it is not GROMACS specific
please ask on the mailinglist of your MPI library. If it only happens with
GROMACS be more specific about what your setup is (what MPI library, what
hardware, ...).

Also you could use the latest GROMACS 4.5.x. It has built in thread support
and doesn't need MPI as long as you only run on n cores within one SMP node.

Roland

On Wed, Apr 27, 2011 at 2:13 PM, Hrachya Astsatryan  wrote:

> Dear Mark Abraham & all,
>
> We  used another benchmarking systems, such as d.dppc on 4 processors, but
> we have the same problem (1 proc use about 100%, the others 0%).
> After for a while we receive the following error:
>
> Working directory is /localuser/armen/d.dppc
> Running on host wn1.ysu-cluster.grid.am
> Time is Fri Apr 22 13:55:47 AMST 2011
> Directory is /localuser/armen/d.dppc
> START
> Start: Fri Apr 22 13:55:47 AMST 2011
> p2_487:  p4_error: Timeout in establishing connection to remote process: 0
> rm_l_2_500: (301.160156) net_send: could not write to fd=5, errno = 32
> p2_487: (301.160156) net_send: could not write to fd=5, errno = 32
> p0_32738:  p4_error: net_recv read:  probable EOF on socket: 1
> p3_490: (301.160156) net_send: could not write to fd=6, errno = 104
> p3_490:  p4_error: net_send write: -1
> p3_490: (305.167969) net_send: could not write to fd=5, errno = 32
> p0_32738: (305.371094) net_send: could not write to fd=4, errno = 32
> p1_483:  p4_error: net_recv read:  probable EOF on socket: 1
> rm_l_1_499: (305.167969) net_send: could not write to fd=5, errno = 32
> p1_483: (311.171875) net_send: could not write to fd=5, errno = 32
> Fri Apr 22 14:00:59 AMST 2011
> End: Fri Apr 22 14:00:59 AMST 2011
> END
>
> We tried new version of Gromacs, but receive the same error.
> Please, help us to overcome the problem.
>
>
> With regards,
> Hrach
>
>
> On 4/22/11 1:41 PM, Mark Abraham wrote:
>
>> On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote:
>>
>>> Dear all,
>>>
>>> I would like to inform you that I have installed the gromacs4.0.7 package
>>> on the cluster (nodes of the cluster are 8 core Intel, OS: RHEL4 Scientific
>>> Linux) with the following steps:
>>>
>>> yum install fftw3 fftw3-devel
>>> ./configure --prefix=/localuser/armen/gromacs --enable-mpi
>>>
>>> Also I have downloaded gmxbench-3.0 package and try to run d.villin to
>>> test it.
>>>
>>> Unfortunately it wok fine until np is 1,2,3, if I use more than 3 procs I
>>> receive low CPU balancing and the process in hanging.
>>>
>>> Could you, please, help me to overcome the problem?
>>>
>>
>> Probably you have only four physical cores (hyperthreading is not normally
>> useful), or your MPI is configured to use only four cores, or these
>> benchmarks are too small to scale usefully.
>>
>> Choosing to do a new installation of a GROMACS version that is several
>> years old is normally less productive than the latest version.
>>
>> Mark
>>
>>
>>
>>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
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>
>
>


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Re: [gmx-users] Help: Gromacs Installation

[Hrachya Astsatryan]

Dear Mark Abraham & all,

We  used another benchmarking systems, such as d.dppc on 4 processors, 
but we have the same problem (1 proc use about 100%, the others 0%).

After for a while we receive the following error:

Working directory is /localuser/armen/d.dppc
Running on host wn1.ysu-cluster.grid.am
Time is Fri Apr 22 13:55:47 AMST 2011
Directory is /localuser/armen/d.dppc
START
Start: Fri Apr 22 13:55:47 AMST 2011
p2_487:  p4_error: Timeout in establishing connection to remote process: 0
rm_l_2_500: (301.160156) net_send: could not write to fd=5, errno = 32
p2_487: (301.160156) net_send: could not write to fd=5, errno = 32
p0_32738:  p4_error: net_recv read:  probable EOF on socket: 1
p3_490: (301.160156) net_send: could not write to fd=6, errno = 104
p3_490:  p4_error: net_send write: -1
p3_490: (305.167969) net_send: could not write to fd=5, errno = 32
p0_32738: (305.371094) net_send: could not write to fd=4, errno = 32
p1_483:  p4_error: net_recv read:  probable EOF on socket: 1
rm_l_1_499: (305.167969) net_send: could not write to fd=5, errno = 32
p1_483: (311.171875) net_send: could not write to fd=5, errno = 32
Fri Apr 22 14:00:59 AMST 2011
End: Fri Apr 22 14:00:59 AMST 2011
END

We tried new version of Gromacs, but receive the same error.
Please, help us to overcome the problem.


With regards,
Hrach

On 4/22/11 1:41 PM, Mark Abraham wrote:

On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote:

Dear all,

I would like to inform you that I have installed the gromacs4.0.7 
package on the cluster (nodes of the cluster are 8 core Intel, OS: 
RHEL4 Scientific Linux) with the following steps:


yum install fftw3 fftw3-devel
./configure --prefix=/localuser/armen/gromacs --enable-mpi

Also I have downloaded gmxbench-3.0 package and try to run d.villin 
to test it.


Unfortunately it wok fine until np is 1,2,3, if I use more than 3 
procs I receive low CPU balancing and the process in hanging.


Could you, please, help me to overcome the problem?


Probably you have only four physical cores (hyperthreading is not 
normally useful), or your MPI is configured to use only four cores, or 
these benchmarks are too small to scale usefully.


Choosing to do a new installation of a GROMACS version that is several 
years old is normally less productive than the latest version.


Mark





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Re: [gmx-users] Help: Gromacs Installation

[Mark Abraham]

On 4/22/2011 5:40 PM, Hrachya Astsatryan wrote:

Dear all,

I would like to inform you that I have installed the gromacs4.0.7 
package on the cluster (nodes of the cluster are 8 core Intel, OS: 
RHEL4 Scientific Linux) with the following steps:


yum install fftw3 fftw3-devel
./configure --prefix=/localuser/armen/gromacs --enable-mpi

Also I have downloaded gmxbench-3.0 package and try to run d.villin to 
test it.


Unfortunately it wok fine until np is 1,2,3, if I use more than 3 
procs I receive low CPU balancing and the process in hanging.


Could you, please, help me to overcome the problem?


Probably you have only four physical cores (hyperthreading is not 
normally useful), or your MPI is configured to use only four cores, or 
these benchmarks are too small to scale usefully.


Choosing to do a new installation of a GROMACS version that is several 
years old is normally less productive than the latest version.


Mark



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Mark Abraham]

On 7/04/2011 9:38 PM, Peter C. Lai wrote:

Ok here's a minor? problem I'm having with dihedrals.

Apparently grompp won't read H-H dihedrals such as:

HGA2   CG321  CG321  HGA2   9   0.000.92048 3 ;LIPID alkane
HGA2   CG321  CG331  HGA3   9   0.000.66944 3 ;PROT rotation 
barrier in ethane
(the lipid equiv would be: HAL2 CTL2 CTL2 HAL2)

it only seems to work if I use
X CG321 CG321 X
but that always seems a bit too broadspectrum...

I'm not using heavy H or anything, just a normal pdb2gmx and normal grompp
but it complains about the H-H dihedrals as "No default Proper Dih. types"...

Any ideas?


So the relevant hydrogen atoms do not have type HGA2 or HGA3, or you're 
not using the right files. Perhaps the error message says what line of 
the .itp is causing problems...


Mark
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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Peter C. Lai]

Ok here's a minor? problem I'm having with dihedrals.

Apparently grompp won't read H-H dihedrals such as:

HGA2   CG321  CG321  HGA2   9   0.000.92048 3 ;LIPID alkane
HGA2   CG321  CG331  HGA3   9   0.000.66944 3 ;PROT rotation 
barrier in ethane
(the lipid equiv would be: HAL2 CTL2 CTL2 HAL2)

it only seems to work if I use
X CG321 CG321 X
but that always seems a bit too broadspectrum...

I'm not using heavy H or anything, just a normal pdb2gmx and normal grompp
but it complains about the H-H dihedrals as "No default Proper Dih. types"...

Any ideas?
-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Mark Abraham]

On 7/04/2011 5:39 PM, Peter C. Lai wrote:

Actually I figured it out.

in forcefield.itp,

the nonbonded.itp file must be included before the bonded.itp file...


Yep, it has the [atomtypes].

Mark


On 2011-04-07 02:22:38AM -0500, Mark Abraham wrote:

On 7/04/2011 3:45 PM, Peter C. Lai wrote:

Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"
grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated
a gro and a top file:

http://pastebin.com/HL3k7EPU for the gro
http://pastebin.com/y6T4ir7y for the top

I ran "grompp -f em.mdp -c nonanone.gro -p nonanone.top -o em.tpr"

CG2O5 and all the other new atoms I added are in the appropriate
atomtypes.atp file. The forcefield.itp file I added my custom #includes
for the new parameters.

How do I go about tracing this?

You need to be sure your grompp working directory also has the modified
forcefield file. The "include path" for filenames looks first in the
working directory and then in the directory indicated when you sourced
GMXRC. grompp's normal output (or maybe with -debug 1, or something)
probably says what it is doing.

grompp -pp will write a post-processed stand-alone .top that you can use
to verify things got picked up correctly. However if grompp is failing,
that's probably not a help.

Mark


the rtp is correct since it wouldn't have been able to map NNON to a gro
and top file otherwise.

Here is my forcefield.itp:
http://pastebin.com/6dTKuqnG

The two files I custom added were ffgenbonded.itp and ffgennonbonded.itp
http://pastebin.com/xYvXtbzT
http://pastebin.com/XXAbmvRH

Any help would be greatly appreciated...

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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Peter C. Lai]

Actually I figured it out.

in forcefield.itp,

the nonbonded.itp file must be included before the bonded.itp file...

On 2011-04-07 02:22:38AM -0500, Mark Abraham wrote:
> On 7/04/2011 3:45 PM, Peter C. Lai wrote:
> > Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"
> > grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated
> > a gro and a top file:
> >
> > http://pastebin.com/HL3k7EPU for the gro
> > http://pastebin.com/y6T4ir7y for the top
> >
> > I ran "grompp -f em.mdp -c nonanone.gro -p nonanone.top -o em.tpr"
> >
> > CG2O5 and all the other new atoms I added are in the appropriate
> > atomtypes.atp file. The forcefield.itp file I added my custom #includes
> > for the new parameters.
> >
> > How do I go about tracing this?
> 
> You need to be sure your grompp working directory also has the modified 
> forcefield file. The "include path" for filenames looks first in the 
> working directory and then in the directory indicated when you sourced 
> GMXRC. grompp's normal output (or maybe with -debug 1, or something) 
> probably says what it is doing.
> 
> grompp -pp will write a post-processed stand-alone .top that you can use 
> to verify things got picked up correctly. However if grompp is failing, 
> that's probably not a help.
> 
> Mark
> 
> > the rtp is correct since it wouldn't have been able to map NNON to a gro
> > and top file otherwise.
> >
> > Here is my forcefield.itp:
> > http://pastebin.com/6dTKuqnG
> >
> > The two files I custom added were ffgenbonded.itp and ffgennonbonded.itp
> > http://pastebin.com/xYvXtbzT
> > http://pastebin.com/XXAbmvRH
> >
> > Any help would be greatly appreciated...
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Peter C. Lai]

On 2011-04-07 02:01:47AM -0500, Mark Abraham wrote:
> On 7/04/2011 3:45 PM, Peter C. Lai wrote:
> > Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"
> 
> On what line of what file? Please copy and paste the whole error 
> message. Keeping information back only hurts you :-)

Here is the entire message. It doesn't give me a line number in the
mdp file

NOTE 1 [file em.mdp]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rcoulomb.


---
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 631

Fatal error:
Unknown bond_atomtype CG2O5

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


> 
> Mark
> 
> > grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated
> > a gro and a top file:
> >
> > http://pastebin.com/HL3k7EPU for the gro
> > http://pastebin.com/y6T4ir7y for the top
> >
> > I ran "grompp -f em.mdp -c nonanone.gro -p nonanone.top -o em.tpr"
> >
> > CG2O5 and all the other new atoms I added are in the appropriate
> > atomtypes.atp file. The forcefield.itp file I added my custom #includes
> > for the new parameters.
> >
> > How do I go about tracing this?
> > the rtp is correct since it wouldn't have been able to map NNON to a gro
> > and top file otherwise.
> >
> > Here is my forcefield.itp:
> > http://pastebin.com/6dTKuqnG
> >
> > The two files I custom added were ffgenbonded.itp and ffgennonbonded.itp
> > http://pastebin.com/xYvXtbzT
> > http://pastebin.com/XXAbmvRH
> >
> > Any help would be greatly appreciated...
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Mark Abraham]

On 7/04/2011 3:45 PM, Peter C. Lai wrote:

Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"
grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated
a gro and a top file:

http://pastebin.com/HL3k7EPU for the gro
http://pastebin.com/y6T4ir7y for the top

I ran "grompp -f em.mdp -c nonanone.gro -p nonanone.top -o em.tpr"

CG2O5 and all the other new atoms I added are in the appropriate
atomtypes.atp file. The forcefield.itp file I added my custom #includes
for the new parameters.

How do I go about tracing this?


You need to be sure your grompp working directory also has the modified 
forcefield file. The "include path" for filenames looks first in the 
working directory and then in the directory indicated when you sourced 
GMXRC. grompp's normal output (or maybe with -debug 1, or something) 
probably says what it is doing.


grompp -pp will write a post-processed stand-alone .top that you can use 
to verify things got picked up correctly. However if grompp is failing, 
that's probably not a help.


Mark


the rtp is correct since it wouldn't have been able to map NNON to a gro
and top file otherwise.

Here is my forcefield.itp:
http://pastebin.com/6dTKuqnG

The two files I custom added were ffgenbonded.itp and ffgennonbonded.itp
http://pastebin.com/xYvXtbzT
http://pastebin.com/XXAbmvRH

Any help would be greatly appreciated...


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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Mark Abraham]

On 7/04/2011 3:45 PM, Peter C. Lai wrote:

Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5"


On what line of what file? Please copy and paste the whole error 
message. Keeping information back only hurts you :-)


Mark


grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated
a gro and a top file:

http://pastebin.com/HL3k7EPU for the gro
http://pastebin.com/y6T4ir7y for the top

I ran "grompp -f em.mdp -c nonanone.gro -p nonanone.top -o em.tpr"

CG2O5 and all the other new atoms I added are in the appropriate
atomtypes.atp file. The forcefield.itp file I added my custom #includes
for the new parameters.

How do I go about tracing this?
the rtp is correct since it wouldn't have been able to map NNON to a gro
and top file otherwise.

Here is my forcefield.itp:
http://pastebin.com/6dTKuqnG

The two files I custom added were ffgenbonded.itp and ffgennonbonded.itp
http://pastebin.com/xYvXtbzT
http://pastebin.com/XXAbmvRH

Any help would be greatly appreciated...


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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Peter C. Lai]

Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5" 
grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated
a gro and a top file:

http://pastebin.com/HL3k7EPU for the gro
http://pastebin.com/y6T4ir7y for the top

I ran "grompp -f em.mdp -c nonanone.gro -p nonanone.top -o em.tpr"

CG2O5 and all the other new atoms I added are in the appropriate
atomtypes.atp file. The forcefield.itp file I added my custom #includes
for the new parameters.

How do I go about tracing this?
the rtp is correct since it wouldn't have been able to map NNON to a gro
and top file otherwise.

Here is my forcefield.itp:
http://pastebin.com/6dTKuqnG

The two files I custom added were ffgenbonded.itp and ffgennonbonded.itp
http://pastebin.com/xYvXtbzT
http://pastebin.com/XXAbmvRH

Any help would be greatly appreciated...
-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

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Re: [gmx-users] Help with using g_bar

[Justin A. Lemkul]

Warren Gallin wrote:

On 2011-04-06, at 10:58 AM, Justin A. Lemkul wrote:



Warren Gallin wrote:

I am trying to use g_bar to derive a PMF curve from non-equilibrium
trajectory data.  I am using v 4.5.4 on a Mac running OSX 10.6.7.
I am using the end-to-end distance of a peptide as the co-ordinate of
interest.  After doing a long simulation of the peptide, I selected the
frames with the longest and shortest end-to-end distances, imposed a
restraint on the end-to-end distance by adding a type 10 bond centered on the
end-toend distance in the farme with a large force constant to the topology,
and then ran a simulation to generate an ensemble of conformations with the
end-to-end distances restrained at the longest and shortest distances.
I then selected 5 frames from each of those two simulations and used those as
the starting conformations for 20 ps simulations with free_energy set to yes
with the end-to-end distance changing linearly with lambda between the two
distances, with 11 equally spaced foreign_lambda values, from 0 to 1.0.  I
got what I thought would be tyhe expected dhdl files (see two attached files,
one for short-to-long and the other for long-to-short).
However, when I invoke g_bar with these ten files as input I get no PMF, the
free energy difference between the longest and shortest distances is printed
out as zero, and I get a histogram file with extensive overlap.
So, I must be making a mistake in either choosing the simulation parameters
for the non-equilibrium trajectories or I am misunderstanding what g_bar is
supposed to do, or 5 simulations in each direction is not enough to get any
kind of output.  Note, I realize that I will need to run many more
non-equilibrium runs to get a reliable analysis, but I am just trying to run
a minimal test to be sure that I am not off on the wrong track.
Could someone suggest where I am going wrong, and even better where I might
find some documentation of the operational use of g_bar?

A complete .mdp file would help.  I'm guessing you didn't set foreign_lambda 
for any of these simulations?  g_bar works by evaluating energies at native and 
foreign lambda values.


foreign_lambda was set, hence all the ∆H curves.

I've attached the .mdp file for both directions of the simulation.



OK, you've got a lot going on here:

init_lambda =  1
delta_lambda=  -.0001
free_energy =  yes
foreign_lambda  =  0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0

You're changing lambda as a function of time, and assigning a value of 1 to both 
foreign and native lambda.  More reliable settings have been discussed within 
the last few days, i.e.:


http://lists.gromacs.org/pipermail/gmx-users/2011-March/059694.html

So I would suggest you turn off the slow growth setting (since I am not sure how 
it will affect the BAR results, and because it's error-prone), and if that 
doesn't fix it, split the transformation into a few separate simulations at 
defined intervals of native lambda and foreign lambda (such that they don't 
overlap, either).


-Justin





A tutorial is in the works (but not for this specific application; free energy 
simulations in general).  No promises on when it will be done, but hopefully 
very soon.

-Justin


Thanks,
Warren Gallin














--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help with using g_bar

[Warren Gallin]

On 2011-04-06, at 10:58 AM, Justin A. Lemkul wrote:

> 
> 
> Warren Gallin wrote:
>> I am trying to use g_bar to derive a PMF curve from non-equilibrium
>> trajectory data.  I am using v 4.5.4 on a Mac running OSX 10.6.7.
>> I am using the end-to-end distance of a peptide as the co-ordinate of
>> interest.  After doing a long simulation of the peptide, I selected the
>> frames with the longest and shortest end-to-end distances, imposed a
>> restraint on the end-to-end distance by adding a type 10 bond centered on the
>> end-toend distance in the farme with a large force constant to the topology,
>> and then ran a simulation to generate an ensemble of conformations with the
>> end-to-end distances restrained at the longest and shortest distances.
>> I then selected 5 frames from each of those two simulations and used those as
>> the starting conformations for 20 ps simulations with free_energy set to yes
>> with the end-to-end distance changing linearly with lambda between the two
>> distances, with 11 equally spaced foreign_lambda values, from 0 to 1.0.  I
>> got what I thought would be tyhe expected dhdl files (see two attached files,
>> one for short-to-long and the other for long-to-short).
>> However, when I invoke g_bar with these ten files as input I get no PMF, the
>> free energy difference between the longest and shortest distances is printed
>> out as zero, and I get a histogram file with extensive overlap.
>> So, I must be making a mistake in either choosing the simulation parameters
>> for the non-equilibrium trajectories or I am misunderstanding what g_bar is
>> supposed to do, or 5 simulations in each direction is not enough to get any
>> kind of output.  Note, I realize that I will need to run many more
>> non-equilibrium runs to get a reliable analysis, but I am just trying to run
>> a minimal test to be sure that I am not off on the wrong track.
>> Could someone suggest where I am going wrong, and even better where I might
>> find some documentation of the operational use of g_bar?
> 
> A complete .mdp file would help.  I'm guessing you didn't set foreign_lambda 
> for any of these simulations?  g_bar works by evaluating energies at native 
> and foreign lambda values.

foreign_lambda was set, hence all the ∆H curves.

I've attached the .mdp file for both directions of the simulation.



> 
> A tutorial is in the works (but not for this specific application; free 
> energy simulations in general).  No promises on when it will be done, but 
> hopefully very soon.
> 
> -Justin
> 
>> Thanks,
>> Warren Gallin
>> 
> 



run.mdp
Description: Binary data




run_bar_l.mdp
Description: Binary data

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Re: [gmx-users] Help with using g_bar

[Justin A. Lemkul]

Warren Gallin wrote:

I am trying to use g_bar to derive a PMF curve from non-equilibrium
trajectory data.  I am using v 4.5.4 on a Mac running OSX 10.6.7.

I am using the end-to-end distance of a peptide as the co-ordinate of
interest.  After doing a long simulation of the peptide, I selected the
frames with the longest and shortest end-to-end distances, imposed a
restraint on the end-to-end distance by adding a type 10 bond centered on the
end-toend distance in the farme with a large force constant to the topology,
and then ran a simulation to generate an ensemble of conformations with the
end-to-end distances restrained at the longest and shortest distances.

I then selected 5 frames from each of those two simulations and used those as
the starting conformations for 20 ps simulations with free_energy set to yes
with the end-to-end distance changing linearly with lambda between the two
distances, with 11 equally spaced foreign_lambda values, from 0 to 1.0.  I
got what I thought would be tyhe expected dhdl files (see two attached files,
one for short-to-long and the other for long-to-short).

However, when I invoke g_bar with these ten files as input I get no PMF, the
free energy difference between the longest and shortest distances is printed
out as zero, and I get a histogram file with extensive overlap.

So, I must be making a mistake in either choosing the simulation parameters
for the non-equilibrium trajectories or I am misunderstanding what g_bar is
supposed to do, or 5 simulations in each direction is not enough to get any
kind of output.  Note, I realize that I will need to run many more
non-equilibrium runs to get a reliable analysis, but I am just trying to run
a minimal test to be sure that I am not off on the wrong track.

Could someone suggest where I am going wrong, and even better where I might
find some documentation of the operational use of g_bar?



A complete .mdp file would help.  I'm guessing you didn't set foreign_lambda for 
any of these simulations?  g_bar works by evaluating energies at native and 
foreign lambda values.


A tutorial is in the works (but not for this specific application; free energy 
simulations in general).  No promises on when it will be done, but hopefully 
very soon.


-Justin


Thanks,

Warren Gallin








--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Peter C. Lai]

On 2011-04-06 01:49:50AM -0500, Mark Abraham wrote:
> The standard CHARMM .prm files give an indication of how the parameters 
> will be used, so it's just a matter of converting units and taking care 
> of any constants.

Looks like if I use
http://lists.gromacs.org/pipermail/gmx-users/2010-September/054302.html
for sigma/epsilon, I'll need to divide the converted sigma by 10 now...

Looks like for eps1,4 I take the eps1,4 of each atom in the pair,
sqrt(charmm(eps1,4i)*charmm(eps1,4j))*4.184

And for the sigma1,4 term I take the sum of the Rmin/2, divide by 2 
then convert to sigma per pair.

For the dihedrals, it looks like 
gromacs(phi0) = charmm(delta)
and
gromacs(cp) = charmm(Kchi)*4.184

And for impropers
gromacs(cp) = charmm(Kpsi)*4.184*2

At least those look like the calculations done for the c36ff conversion.

Thanks for your help!
-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Thomas Piggot]

Yes, Mark is exactly correct about the glitch. I had just forgotten to 
change this default charge in the ffnonbonded.itp when copying from 
another atom. As mentioned this has no impact as these charges are never 
used by pdb2gmx.


Cheers

Tom

Mark Abraham wrote:

On 6/04/2011 2:51 PM, Peter C. Lai wrote:

Hello

I am constructing a ligand for which I wish to use the new Charmm CGenFF
parameters (a long aliphatic ketone).

I am using Tom/Par's charmm36 lipid conversion as a baseline template for
comparison:

For reference, c36 lipid CTL3 atoms (in the case of POPC) map to CG331
in CGenFF; they are both to represent alkane CH3 carbons. Same with
CTL2 ->  CG321. In my case I am particularly interested in CGenFF's
parameterization of a ketone carbonyl and oxygen: CG2O5 and OG2D3
(without any associated carboxylic bias or bias from non-carbons found
in other parameters. For example C=O in amino acid backbone appears in
ffbonded.itp as 5.188e+05 for kB whereas Mark's script yielded a kB of
5.858e+05 for CG2O5=OG2D3, not to mention the bond angles should be
different and especially the nonbonded interactions since we've replaced
N with C and we have an extra H etc. etc.).

My ligand for now is pretty simple:

   OG2D3
||
CG331-CG321-...-CG321-CG2O5-CG331

or, in c36 lipid/prot terms:
O
||
CTL3-CTL2-...-CTL2-C-C-CTL3

How would I convert the relevant atoms in CGenFF's prm file to both
dihedral and nonbonded interaction .itp for gromacs?


The standard CHARMM .prm files give an indication of how the parameters 
will be used, so it's just a matter of converting units and taking care 
of any constants.



  I tried using Mark's
perl scripts and it is giving me wrong LJ terms as well as not picking up
any 1,4 interactions (not to mention it has no knowledge of Par's
functype 9 for converting Charmm dihderals - we should no longer be using
R-B functions).


This script predates dihedral functype 9, and implements a 
post-processing approach to deal with LJ, 1-4 and some dihedrals. I 
assume you haven't done the latter. In any case, the form of my 
solutions do not mesh at all with Par's solutions - forget about my scripts.


You seem to be only interested in about two atom types, so I'd expect 
you can convert all the relevant things by hand in under an hour.



Finally, a slightly (un)related question:
in ffnonbonded.itp, why does CTL2 get a charge of 0.05 when in reality we
usually give it -0.18 for associated molecules in the rtp? Is there
something I'm missing there? (CTL3 has -0.27 in both the itp and rtp files
which makes sense to me).


Sounds like a glitch when the file was written - I guess some other 
carbon also has 0.05 and this was copied and pasted. In any case, the 
charges in ffnonbonded.itp are never used by pdb2gmx, because 
precedence-taking residue-specific charges are defined in the .rtp. If 
one were to use some other tool for generating topologies, I don't know 
whether charges missing from a [moleculetype] definition are looked up 
in ffnonbonded.itp.


Mark


--
Dr Thomas Piggot
University of Southampton, UK.
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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Mark Abraham]

On 6/04/2011 2:51 PM, Peter C. Lai wrote:

Hello

I am constructing a ligand for which I wish to use the new Charmm CGenFF
parameters (a long aliphatic ketone).

I am using Tom/Par's charmm36 lipid conversion as a baseline template for
comparison:

For reference, c36 lipid CTL3 atoms (in the case of POPC) map to CG331
in CGenFF; they are both to represent alkane CH3 carbons. Same with
CTL2 ->  CG321. In my case I am particularly interested in CGenFF's
parameterization of a ketone carbonyl and oxygen: CG2O5 and OG2D3
(without any associated carboxylic bias or bias from non-carbons found
in other parameters. For example C=O in amino acid backbone appears in
ffbonded.itp as 5.188e+05 for kB whereas Mark's script yielded a kB of
5.858e+05 for CG2O5=OG2D3, not to mention the bond angles should be
different and especially the nonbonded interactions since we've replaced
N with C and we have an extra H etc. etc.).

My ligand for now is pretty simple:

   OG2D3
||
CG331-CG321-...-CG321-CG2O5-CG331

or, in c36 lipid/prot terms:
O
||
CTL3-CTL2-...-CTL2-C-C-CTL3

How would I convert the relevant atoms in CGenFF's prm file to both
dihedral and nonbonded interaction .itp for gromacs?


The standard CHARMM .prm files give an indication of how the parameters 
will be used, so it's just a matter of converting units and taking care 
of any constants.



  I tried using Mark's
perl scripts and it is giving me wrong LJ terms as well as not picking up
any 1,4 interactions (not to mention it has no knowledge of Par's
functype 9 for converting Charmm dihderals - we should no longer be using
R-B functions).


This script predates dihedral functype 9, and implements a 
post-processing approach to deal with LJ, 1-4 and some dihedrals. I 
assume you haven't done the latter. In any case, the form of my 
solutions do not mesh at all with Par's solutions - forget about my scripts.


You seem to be only interested in about two atom types, so I'd expect 
you can convert all the relevant things by hand in under an hour.



Finally, a slightly (un)related question:
in ffnonbonded.itp, why does CTL2 get a charge of 0.05 when in reality we
usually give it -0.18 for associated molecules in the rtp? Is there
something I'm missing there? (CTL3 has -0.27 in both the itp and rtp files
which makes sense to me).


Sounds like a glitch when the file was written - I guess some other 
carbon also has 0.05 and this was copied and pasted. In any case, the 
charges in ffnonbonded.itp are never used by pdb2gmx, because 
precedence-taking residue-specific charges are defined in the .rtp. If 
one were to use some other tool for generating topologies, I don't know 
whether charges missing from a [moleculetype] definition are looked up 
in ffnonbonded.itp.


Mark
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Re: [gmx-users] Help with Umbrella Sampling

[Justin A. Lemkul]

Raghuvir R S Pissurlenkar wrote:

Dear Justin

I removed the constrain on the DPPC molecules, however I find still 
LINCS errors are prominent

Any alterative can I try



Reduce the pull_rate.  If you pull too fast, your system cannot adapt properly 
to the collisions that are induced by the artificial force.


-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help on umbrella sampling

[Justin A. Lemkul]

raghu...@bcpindia.org wrote:

Dear Users and Developers

I am trying to execute md_pull.mdp {given below} on a small molecule 
embedded at the core of lipid bilayer.  I have tried to modify the 
md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling.  I 
encounter LINCS warning  (1000) after about 100-110 ps of the simulation 
resulting in termination of mdrun. This occurs when the small molecule 
is near the polar heads.  I understand the system is exploding.


I have minimized the system, followed by anneal to 323K then nvt and npt 
after which I perform the md_pull.  How can I soften the core {as 
mentioned in the errors on www.gromacs.org} or any other alternative is 
there adding lincs warning to mdp file {I am not aware}




"Soft core" is a mechanism by which Lennard-Jones interactions are modified 
while doing decoupling/annihilation calculations.  This point is not relevant here.


I see that you're restraining the lipids in some way.  Which atoms are 
restrained?  In which directions?  Why are you restraining them?  I would assume 
that as a molecule is pulled through your membrane, any artificial forces that 
work against one another would cause instability.


-Justin


Following is the md_pull.mdp file as modified;
X
title= Umbrella pulling simulation
define= -DPOSRES_DPPC
; Run parameters
integrator= md
dt= 0.002
tinit= 0
nsteps= 10; 200 ps
nstcomm= 1
; Output parameters
nstxout= 5000; every 10 ps
nstvout= 5000
nstfout= 500
nstxtcout= 500; every 1 ps
nstenergy= 500
; Bond parameters
constraint_algorithm = lincs
constraints= all-bonds
continuation = yes; continuing from NPT
; Single-range cutoff scheme
nstlist= 5
ns_type= grid
rlist= 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype= PME
fourierspacing  = 0.12
fourier_nx= 0
fourier_ny = 0
fourier_nz= 0
pme_order= 4
ewald_rtol= 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl =Nose-Hoover
tc_grps=TPFDPPCSOL
tau_t=0.10.10.1
ref_t=323323323
; Pressure coupling is on
pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype= semiisotropic; uniform scaling of x-y box 
vectors, independent z

tau_p= 2.0; time constant, in ps
ref_p= 1.01.0; reference pressure, x-y, z 
(in bar)

compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1
; Generate velocities is off
gen_vel= no
; Periodic boundary conditions are on in all directions
pbc= xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry= distance
pull_dim= N N Y
pull_start= yes; define initial COM distance > 0
pull_ngroups= 1
pull_group0= DPPC
pull_group1= TPF
pull_rate1= 0.01; 0.01 nm per ps = 10 nm per ns
pull_k1= 1000; kJ mol^-1 nm^-2
XX
Please help me

Thanks N Regards

Raghuvir



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help regarding terinary complex simulation with ZN at active site

[Justin A. Lemkul]

kala wrote:

Dear friends

I am trying to run a MD simulation with a Zn ion in the 
active site. The zinc makes covalent bond to His , Asp , Cys and Drug 
molecule. however I am trying to study various ligands that make a 
sustainable bond with zn over period of time. I am new to gmx and I am 
pretty confused with .rtp and specbond.dat . How should I make His (its 
actually HisD) , Asp and Cys bonded with Zn and enough residual charge 
on zn with which it can form a bond to ligand molecule. will definitions 


Bonds do not break or form during MD, unless you are doing QM/MM.

of bond lengths and bond angles on specbond.dat will alone suffice ? I 
am using Amber99sb ff so that I can carry out md on my fermi card. any 
help is highly appreciated.


You can define bonds in specbond.dat between your protein residues and the Zn 
ion, but there are no bonded parameters for such interactions in that force 
field, by default.  Thus you will either have to parameterize them yourself or 
define some arbitrary distance restraints (thus not using specbond.dat).


You also face the challenge that in such a species there will likely be 
significant inductive effects requiring a re-parameterization of the active 
site.  What's more, a static representation of these charges may not be 
sufficiently accurate.  There are various QM/MM papers that have shown this.


Take note of the points raised in the "Exotic species" entry here:

http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin



thanks and regards
bharath



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] Help please.

[Dallas Warren]

Best place to start is to provide an exact copy paste of the command you
used, then an exact copy/paste of the error message.

 

A good resource for errors is
http://www.gromacs.org/Documentation/Errors and searching the emailing
list http://www.gromacs.org/Support/Mailing_Lists/Search 

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Brody Bessire
Sent: Friday, 25 February 2011 8:52 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Help please.

 

Hello all, 

 

I am an undergrad student and I am trying to learn how to run gromacs.
My computer knowledge is somewhat limited so please have patience with
me.

 

I have been trying to run through the initial tutorial right now I am at
the preprocessing of cpeptide with grompp and I keep getting an error
stating that no molecules where defined in the system. What does that
mean? I can provide more detail if prompted but I dont even know what
direction to head in search of touble shooting. Thank you. 

 

 

Brody 

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Re: [gmx-users] Help with B2AR within the POPC membrane

[Aldo Segura]

Dear Justin,

You're right, I corrected the box vectors , and it works!

Thanks,
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Re: [gmx-users] Help with B2AR within the POPC membrane

[Justin A. Lemkul]

Aldo Segura wrote:

Thanks for your answer. You're right in the procedure for the packing
of the protein and lipids. However, after several iterations (~30) the
lipids are packaged to form the bilayer and the protein is outside of
it. I can send you a couple of pictures for a better explanation of my
problem.




That typically happens when either (1) the box vectors are not set correctly 
during system construction or (2) the protein is not properly positioned in the box.


-Justin




Best regards,


Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegu...@ipn.mx; aldoseg...@gmail.com



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help with B2AR within the POPC membrane

[Aldo Segura]

Thanks for your answer. You're right in the procedure for the packing
of the protein and lipids. However, after several iterations (~30) the
lipids are packaged to form the bilayer and the protein is outside of
it. I can send you a couple of pictures for a better explanation of my
problem.




Best regards,


Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegu...@ipn.mx; aldoseg...@gmail.com
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Re: [gmx-users] Help with B2AR within the POPC membrane

[Justin A. Lemkul]

Aldo Segura wrote:

Dear gmxusers,

I need to perform molecular dynamics simulation of a B2AR within the
POPC membrane. I have downloaded the 128b.pdb, popc.itp and lipid.itp
files from Prof.Tieleman's group. My protein of interest is 343
residues. Also, I aligned the protein and membrane. I followed the
Justin Lemkul tutorial for KALP-15. The result of inflate.gro is in
agreement with the result showed in the tutorial (Visual inspection
with VMD). However, the result of the first minimization shows that
the protein and lipids are separated rather than starting to pack. I'm
using gromacs-4.5.3.

Can someone help me?



Energy minimization does not pack the lipids around the protein.  You have to do 
numerous iterations of shrinking + EM to accomplish this.  There is a protocol 
in the tutorial for this.  Or is there some other problem?


-Justin


my minim.mdp file:

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
define  = -DSTRONG_POSRES ; position restrain the protein
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform

; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and 
long range forces
ns_type = grid  ; Method to determine neighbor list (simple, 
grid)
rlist   = 1.2   ; Cut-off for making neighbor list (short range 
forces)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.2   ; Short-range electrostatic cut-off
rvdw= 1.2   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)


Best regards,


Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegu...@ipn.mx; aldoseg...@gmail.com


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help with the heme group in forcefield gromos53a6

[Justin A. Lemkul]

Tanos Franca wrote:

Dear users,
We are trying to perform a MD simulation of a protein with a heme group 
using the
gromos53a6 force field but, when trying to run grompp, we receive the 
error mesage:

Program grompp, VERSION 4.0.3
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype FE2+ not found

How can it happen if the gromos53a6 force field have parameters to the 
heme group ?

Does someone knows how to fix it ?



I answered this yesterday:

http://lists.gromacs.org/pipermail/gmx-users/2011-January/057678.html

FE2+ does not exist in the standard 53A6 files, so if you've tried to add it, 
you haven't done it right.


-Justin


Tanos Celmar Costa Franca - D.Sc
Coordenador do Programa de Pos-graduacão em Química
Secão de Engenharia Química - SE/5
Instituto Militar de Engenharia - IME
Rio de Janeiro - RJ
Brasil



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] help regarding simulation

[Justin A. Lemkul]

onetwo wrote:

Hello All,

I want to know one thing that if MD could be used in my case, i have a 
protein for which crystal structure is known with a conenzyme bound to 
it. It is given in literature that related proteins of this family shows 
large conformational change near the substrate binding region when the 
substrate binds to the protein.
In absence of the crystal structure, if doing simulation with the 
protein complexed with the coenzyme and the docked substrate will be 
useful? , i.e, if this complex with the help of the simulation could be 
capable of displaying such conformational change ? or what could be the 
probable limitaions ?




Possibly.  The limitation is time.  Conformational changes are generally slow, 
so your simulations would likely have to be fairly long.


-Justin


Regards and thanks for your time.





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help for MD of short peptides at 276K

[Justin A. Lemkul]

Subhrangshu Supakar wrote:

Hi!!

I am new to short peptide simulations at low temperatures.
I want to run a MD of short peptides of 6 - 12 residues at 276 K.
For this the scheme I wish to follow is :
1. Run a short energy minimization of the peptide + water system to 
remove short contacts

2. Equillibrate the system at 2K for 100ps
3. Rum MD with a starting temperature of 2K and finally taking it to 
276K in ~ 120ps in 15 annealing points and continue for ~ 50 - 100 ns


Is this OK or do I have to Equilibrate the system at ~298K and in MD 
take the temp from 2K to 276 K and continue for 50 ns.




And why would you have to do that?  The purpose of equilibration is to relax 
your system under the desired conditions.


The other thing to worry about is whether or not your water model is valid at a 
point just above freezing.


-Justin


Please help. Thanks in advance


Subhrangshu Supakar
India



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Help to run demo- reg

[Mark Abraham]

 On 14/10/2010 7:19 PM, Sathish wrote:

Dear all,
I have installed gromacs 4.5.1 in RHEL5.5 server. Then i was started 
to run demo but still its running ( more then 5 hrs). How long will 
take time to complete.

Any other possible way is there to increase speed ?
Anybody can help me?


It's probably hung because the demo was written well before 4.5 and some 
of the program usages have changed. If you really want to see the demo, 
then compiling GROMACS 4.0.7 will probably work on it.


Mark
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Re: [gmx-users] Help on data anaysis in g_rdf and g_dist

[Justin A. Lemkul]

tekle...@ualberta.ca wrote:

Dear Justine,

As for the distance, have you corrected for PBC? Are you analyzing the 
molecules that you think you are?


No, I did not correct for the PBC. How can I do that. And what is the 
purpose of that in the g_dist calculation.


Usually one uses trjconv.  I'm guessing a bit here, since the only explanation 
you offered was that something "did not look right."  g_dist is one of those 
reliable tools that performs a very simple calculation, so if you think the 
distance should be 0.5 nm, either the trajectory does not agree with your 
conclusion, or you selected something wrong when choosing your analysis groups.




Yes,

I just look at the last frame of my simulation and correctly identified 
the two residues that form aggregates using the sequence viewers in VMD. 
and I developed my index file based on these two. I got the residue name 
and check the group atoms that constitute in the polyaromatic ring of 
these two molecules and calculated the g_dist for ONLY those two 
molecules in the last 1ns.


By default, RDF is done based on atoms, so all atom-atom distances 
will be plotted as part of the RDF. If you want a molecule-based RDF, 
see the options for the -rdf flag.


Yes, I understand that the choise of atom based or molecule based but 
when you said atom-atom based is that for only two molecules or the 
entire 24 molecules in the system ( means the two that form aggregates).




If you're choosing simply "PAP" molecules as the group for analysis (with the 
default -rdf atom), then all atom pairs are considered.  Whether or not that's 
what you want is up to you, but g_rdf is very flexible, so do explore your 
options and consider how best to utilize them.


-Justin


Thank you for you help Justine

Rob

Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:


Dear Gmx users,

After working for quite sometime I managed to simulated almost all my 
molecules for 20ns. Thank you for all your help especially 
Justine.Now I am on last stage of analyzing my data.


First:
I want to calculate g(r)and I used the following command

g_rdf -f PAP_20ns.xtc -s PAP_20ns.tpr -n PAP.ndx -b 19000 -e 2 -o 
result.xvg


Is this right and my data does not look right. For example for the 
PAP-PAP radial distribution function , My data did not converge to 
one at the end it goes all the way to zero. Which is wierd. when I 
made the index file do I need to make for each molecules in the 
system or I cann collectively get the g(r) for all the PAP molecules 
in the system. PAP-PAP RDF for individual molecues in the index file 
or for two separate g(r) is the right value to trust for g(r) of the 
PAP molecule.




By default, RDF is done based on atoms, so all atom-atom distances 
will be plotted as part of the RDF. If you want a molecule-based RDF, 
see the options for the -rdf flag.



Second:

the distance between two polyaromatic rings. I develop a make index 
as follows.


[System]

-
[PAP]
-

[HEP]

[Ring_1]
19 20 21 22 23 24 25 26 27 28 29 30
32 34 37 38 39 40 42 44

[Ring_17]
979 980 981 982 983 984 985 986 987 988 989 990
992 994 997 998 999 1000 1002 1004

Those two rings are the the aggregates in the VMD. I indentified them 
and does the g_dist

between the two but my data looks a little bit off.

g_dist -f PAP_20ns.xtc -s PAP_20ns.tpr -n PAP.ndx -b 19000 -e 2 
-o result.xvg


The value I got is big and does not look right. The diatnce is around 
3.5 nm but if they aggregate it must be a Pi-Pi stacking and should 
be around 0.5 angstrom. Somebody told me i need to develop a script 
to discard some interactions in the pair calculations but did not 
understand what he means ( less ins).




For two non-overlapping groups, this advice does not make sense. 
Intramolecular interactions do count for the RDF calculation, though. 
Perhaps you've gotten your advice confused?


As for the distance, have you corrected for PBC? Are you analyzing the 
molecules that you think you are?


-Justin


Can you please comment on this please. Your help is really appreciated.


Regards,

Rob



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www

Re: [gmx-users] Help on data anaysis in g_rdf and g_dist

[teklebrh]

Dear Justine,

As for the distance, have you corrected for PBC? Are you analyzing  
the molecules that you think you are?


No, I did not correct for the PBC. How can I do that. And what is the  
purpose of that in the g_dist calculation.


Yes,

I just look at the last frame of my simulation and correctly  
identified the two residues that form aggregates using the sequence  
viewers in VMD. and I developed my index file based on these two. I  
got the residue name and check the group atoms that constitute in the  
polyaromatic ring of these two molecules and calculated the g_dist for  
ONLY those two molecules in the last 1ns.


By default, RDF is done based on atoms, so all atom-atom distances  
will be plotted as part of the RDF. If you want a molecule-based  
RDF, see the options for the -rdf flag.


Yes, I understand that the choise of atom based or molecule based but  
when you said atom-atom based is that for only two molecules or the  
entire 24 molecules in the system ( means the two that form aggregates).


Thank you for you help Justine

Rob

Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:


Dear Gmx users,

After working for quite sometime I managed to simulated almost all  
my molecules for 20ns. Thank you for all your help especially  
Justine.Now I am on last stage of analyzing my data.


First:
I want to calculate g(r)and I used the following command

g_rdf -f PAP_20ns.xtc -s PAP_20ns.tpr -n PAP.ndx -b 19000 -e 2  
-o result.xvg


Is this right and my data does not look right. For example for the  
PAP-PAP radial distribution function , My data did not converge to  
one at the end it goes all the way to zero. Which is wierd. when I  
made the index file do I need to make for each molecules in the  
system or I cann collectively get the g(r) for all the PAP  
molecules in the system. PAP-PAP RDF for individual molecues in the  
index file or for two separate g(r) is the right value to trust for  
g(r) of the PAP molecule.




By default, RDF is done based on atoms, so all atom-atom distances  
will be plotted as part of the RDF. If you want a molecule-based  
RDF, see the options for the -rdf flag.



Second:

the distance between two polyaromatic rings. I develop a make index  
as follows.


[System]

-
[PAP]
-

[HEP]

[Ring_1]
19 20 21 22 23 24 25 26 27 28 29 30
32 34 37 38 39 40 42 44

[Ring_17]
979 980 981 982 983 984 985 986 987 988 989 990
992 994 997 998 999 1000 1002 1004

Those two rings are the the aggregates in the VMD. I indentified  
them and does the g_dist

between the two but my data looks a little bit off.

g_dist -f PAP_20ns.xtc -s PAP_20ns.tpr -n PAP.ndx -b 19000 -e 2  
-o result.xvg


The value I got is big and does not look right. The diatnce is  
around 3.5 nm but if they aggregate it must be a Pi-Pi stacking and  
should be around 0.5 angstrom. Somebody told me i need to develop a  
script to discard some interactions in the pair calculations but  
did not understand what he means ( less ins).




For two non-overlapping groups, this advice does not make sense.  
Intramolecular interactions do count for the RDF calculation,  
though. Perhaps you've gotten your advice confused?


As for the distance, have you corrected for PBC? Are you analyzing  
the molecules that you think you are?


-Justin


Can you please comment on this please. Your help is really appreciated.


Regards,

Rob



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Please don't post (un)subscribe requests to the list. Use the www  
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Re: [gmx-users] Help on data anaysis in g_rdf and g_dist

[Justin A. Lemkul]

tekle...@ualberta.ca wrote:


Dear Gmx users,

After working for quite sometime I managed to simulated almost all my 
molecules for 20ns. Thank you for all your help especially Justine.Now I 
am on last stage of analyzing my data.


First:
I want to calculate g(r)and I used the following command

g_rdf -f PAP_20ns.xtc -s PAP_20ns.tpr -n PAP.ndx -b 19000 -e 2 -o 
result.xvg


Is this right and my data does not look right. For example for the 
PAP-PAP radial distribution function , My data did not converge to one 
at the end it goes all the way to zero. Which is wierd. when I made the 
index file do I need to make for each molecules in the system or I cann 
collectively get the g(r) for all the PAP molecules in the system. 
PAP-PAP RDF for individual molecues in the index file or for two 
separate g(r) is the right value to trust for g(r) of the PAP molecule.




By default, RDF is done based on atoms, so all atom-atom distances will be 
plotted as part of the RDF.  If you want a molecule-based RDF, see the options 
for the -rdf flag.



Second:

the distance between two polyaromatic rings. I develop a make index as 
follows.


[System]

-
[PAP]
-

[HEP]

[Ring_1]
  19   20   21   22   23   24   25   26   27   28   29   30
  32   34   37   38   39   40   42   44

[Ring_17]
 979  980  981  982  983  984  985  986  987  988  989  990
 992  994  997  998  999 1000 1002 1004

Those two rings are the the aggregates in the VMD. I indentified them 
and does the g_dist

between the two but my data looks a little bit off.

g_dist -f PAP_20ns.xtc -s PAP_20ns.tpr -n PAP.ndx -b 19000 -e 2 -o 
result.xvg


The value I got is big and does not look right. The diatnce is around 
3.5 nm but if they aggregate it must be a Pi-Pi stacking and should be 
around 0.5 angstrom. Somebody told me i need to develop a script to 
discard some interactions in the pair calculations but did not 
understand what he means ( less ins).




For two non-overlapping groups, this advice does not make sense.  Intramolecular 
interactions do count for the RDF calculation, though.  Perhaps you've gotten 
your advice confused?


As for the distance, have you corrected for PBC?  Are you analyzing the 
molecules that you think you are?


-Justin


Can you please comment on this please. Your help is really appreciated.


Regards,

Rob



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Help on data anaysis in g_rdf and g_dist

[teklebrh]

Dear Gmx users,

After working for quite sometime I managed to simulated almost all my  
molecules for 20ns. Thank you for all your help especially Justine.Now  
I am on last stage of analyzing my data.


First:
I want to calculate g(r)and I used the following command

g_rdf -f PAP_20ns.xtc -s PAP_20ns.tpr -n PAP.ndx -b 19000 -e 2 -o  
result.xvg


Is this right and my data does not look right. For example for the  
PAP-PAP radial distribution function , My data did not converge to one  
at the end it goes all the way to zero. Which is wierd. when I made  
the index file do I need to make for each molecules in the system or I  
cann collectively get the g(r) for all the PAP molecules in the  
system. PAP-PAP RDF for individual molecues in the index file or for  
two separate g(r) is the right value to trust for g(r) of the PAP  
molecule.


Second:

the distance between two polyaromatic rings. I develop a make index as  
follows.


[System]

-
[PAP]
-

[HEP]

[Ring_1]
  19   20   21   22   23   24   25   26   27   28   29   30
  32   34   37   38   39   40   42   44

[Ring_17]
 979  980  981  982  983  984  985  986  987  988  989  990
 992  994  997  998  999 1000 1002 1004

Those two rings are the the aggregates in the VMD. I indentified them  
and does the g_dist

between the two but my data looks a little bit off.

g_dist -f PAP_20ns.xtc -s PAP_20ns.tpr -n PAP.ndx -b 19000 -e 2 -o  
result.xvg


The value I got is big and does not look right. The diatnce is around  
3.5 nm but if they aggregate it must be a Pi-Pi stacking and should be  
around 0.5 angstrom. Somebody told me i need to develop a script to  
discard some interactions in the pair calculations but did not  
understand what he means ( less ins).


Can you please comment on this please. Your help is really appreciated.


Regards,

Rob

--
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Re: [gmx-users] help with git

[Mark Abraham]

- Original Message -
From: Alan 
Date: Wednesday, August 25, 2010 0:10
Subject: Re: [gmx-users] help with git
To: Discussion list for GROMACS users 

> Sorry if confused... because I am *really* confused too with git.
> Anyway, I started anew again and it seems to be working now.> 
> So I clone gmx:> 
> git clone git://git.gromacs.org/gromacs.git  > cd gromacs> git branch> * 
> master> git pull> Already up-to-date.> # now I want to move to 
> 'release-4-5-patch' branch> git checkout -t origin/release-4-5-patches 

If you read the help/manpage for "git checkout" 
(http://www.kernel.org/pub/software/scm/git/docs/git-checkout.html), then you 
will realise you don't want "-t". Tracking of upstream branches is normally set 
up when the branch is created. Rarely, having created a branch, you now want it 
track something upstream, and you can do that too. However, unless you're 
creating branches don't worry about it. These branches already exist - see "git 
branch -a".

I think you just want "git checkout release-4-5-patches" from a fresh clone.

  > Branch release-4-5-patches set up to track remote branch 
release-4-5-patches from origin.> Switched to a new branch 
'release-4-5-patches'> git branch >   master>   * release-4-5-patches> git pull 
> Already up-to-date.> # now I want to go back to master> git checkout -t 
origin/master > fatal: git checkout: branch master already exists

-t is trying to create the branch. So don't do that.

  > git branch   >   master> * release-4-5-patches> # didn't 
change, let's try another command (and here starts my 'guessing' experiment)  > 
git checkout master> Switched to branch 'master'> # nice it works!

Sure.

Mark

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