[gmx-users] Missing bond

[Sudip Das]

Dear All,

While I am preparing my system topology with pdb2gmx for a system
containing enzyme with 30 non-ionic surfactant molecules in water, I got 36
number of bonds per surfactant molecules, but actually it has 37 bonds
(anyways, the number of angle, dihedral etc. are correct). From the
generated topology for this surfactant, I found out the missing bond. But I
checked that I have incorporated that bond in aminoacids.rtp file and that
bond type is also present in the ffbonded.itp file.

To figure out the reason, I used the pdb2gmx for a system with only 30
surfactant molecules in water (no enzyme). Again I encountered the same
problem.

So, what could be the solution? Please assist me.

Thanks in advanced.


Best regards,
Sudip
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[gmx-users] INTERPRETING THE ENERGY VALUES AFTER SIMULATIONS IN GROMACS

[Kulkarni R]

Hi gromacs users,

After protein ligand simulations, I want to do energy analysis.

How to interpret the following data properly? What books and papers should we 
refer?

Energy   AverageErr.Est.   RMSDTot-Drift
---
Coul-SR:Protein-MOL-12.45493.611.7667   -19.8497  (kJ/mol)
LJ-SR:Protein-MOL-103.5021.17.06959 6.6227  (kJ/mol)

What is the significance of total drift?

Can someone offer suggestions and help me to improve?

Thanks,
Kulkarni.R

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Re: [gmx-users] gmx xpm2ps

[Kulkarni R]

Thank you very much



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Diogo Vila 
Viçosa 
Sent: Friday, March 31, 2017 5:00 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx xpm2ps

"gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red" -> "gmx xpm2ps -f
hbmap.xpm -o hbplot.eps -rainbow red"

You have a blanck space between the "-" and the "o".




On Fri, Mar 31, 2017 at 5:52 PM Kulkarni R 
wrote:

> Hi gromacs users,
>
>
> After completing production run, I gave this command
>
>
> gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red
>
>
> However, I got error,
>
>
> ---
> Program: gmx xpm2ps, VERSION 5.1.1
> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> Function:void gmx::CommandLineParser::parse(int*, char**)
>
> Error in user input:
> Invalid command-line options
>   In command-line option -f
> File '-' does not exist or is not accessible.
> The following extensions were tried to complete the file name:
>   .xpm
>   In command-line option -f
> File 'o' does not exist or is not accessible.
> The following extensions were tried to complete the file name:
>   .xpm
>   In command-line option -f
> File name 'hbplot.eps' cannot be used for this option.
> Only the following extensions are possible:
>   .xpm
>
>
> How to avoid this error?
>
> What command should be given preceding to this?
>
> How to get plot of XpixelMap file?
>
>
> Thanks,
>
> Kulkarni.R
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] gmx xpm2ps

[Kulkarni R]

Thank you very much.



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Friday, March 31, 2017 4:52 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx xpm2ps



On 3/31/17 11:27 AM, Kulkarni R wrote:
> Hi gromacs users,
>
>
> After completing production run, I gave this command
>
>
> gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red
>
>
> However, I got error,
>
>
> ---
> Program: gmx xpm2ps, VERSION 5.1.1
> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> Function:void gmx::CommandLineParser::parse(int*, char**)
>
> Error in user input:
> Invalid command-line options
>   In command-line option -f
> File '-' does not exist or is not accessible.
> The following extensions were tried to complete the file name:
>   .xpm
>   In command-line option -f
> File 'o' does not exist or is not accessible.
> The following extensions were tried to complete the file name:
>   .xpm
>   In command-line option -f
> File name 'hbplot.eps' cannot be used for this option.
> Only the following extensions are possible:
>   .xpm
>
>
> How to avoid this error?
>

Don't put a space between - and o in trying to specify the output file,
otherwise you get this incorrect parsing of the command.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
[http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]

Justin A. Lemkul - MacKerell Lab
mackerell.umaryland.edu
Welcome to my site! To learn more about me and the work I am doing, please use 
the navigation links above.



==
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[gmx-users] HYDROGEN BOND EXISTENCE MAP

[Neha Gupta]

Hi gromacs users,

In the perl script to calculate hydrogen bond %, the command is

perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx


What should the structure.pdb file contain?

How to obtain it?

At which point of simulations?

Thanks,
Neha
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Re: [gmx-users] gmx xpm2ps

[Diogo Vila Viçosa]

"gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red" -> "gmx xpm2ps -f
hbmap.xpm -o hbplot.eps -rainbow red"

You have a blanck space between the "-" and the "o".




On Fri, Mar 31, 2017 at 5:52 PM Kulkarni R 
wrote:

> Hi gromacs users,
>
>
> After completing production run, I gave this command
>
>
> gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red
>
>
> However, I got error,
>
>
> ---
> Program: gmx xpm2ps, VERSION 5.1.1
> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> Function:void gmx::CommandLineParser::parse(int*, char**)
>
> Error in user input:
> Invalid command-line options
>   In command-line option -f
> File '-' does not exist or is not accessible.
> The following extensions were tried to complete the file name:
>   .xpm
>   In command-line option -f
> File 'o' does not exist or is not accessible.
> The following extensions were tried to complete the file name:
>   .xpm
>   In command-line option -f
> File name 'hbplot.eps' cannot be used for this option.
> Only the following extensions are possible:
>   .xpm
>
>
> How to avoid this error?
>
> What command should be given preceding to this?
>
> How to get plot of XpixelMap file?
>
>
> Thanks,
>
> Kulkarni.R
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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>
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Re: [gmx-users] gmx xpm2ps

[Justin Lemkul]

On 3/31/17 11:27 AM, Kulkarni R wrote:

Hi gromacs users,


After completing production run, I gave this command


gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red


However, I got error,


---
Program: gmx xpm2ps, VERSION 5.1.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function:void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -f
File '-' does not exist or is not accessible.
The following extensions were tried to complete the file name:
  .xpm
  In command-line option -f
File 'o' does not exist or is not accessible.
The following extensions were tried to complete the file name:
  .xpm
  In command-line option -f
File name 'hbplot.eps' cannot be used for this option.
Only the following extensions are possible:
  .xpm


How to avoid this error?



Don't put a space between - and o in trying to specify the output file, 
otherwise you get this incorrect parsing of the command.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Restraining Protein-ligand distance

[Juan José Galano Frutos]

>
> On 3/27/17 8:42 AM, Juan Jos? Galano Frutos wrote:
> > Hi there,
> >
> > I am trying AFEC simulations in complex (ligand-protein), but sometimes I
> > get the ligands out the binding site, but I dont want that scenary. I was
> > thinking the situation of applying distance retraints between a ligand
> and
> > a protein was already solved in GROMACS version later 5.0... without any
> > necessity of making a hybrid system. But, I'm using version 5.1, and it
> > seems that's not possible doing so, because I'm obtaining errors.
> > Is there currently any happy solution to restraint ligand-protein
> distance?
> > or Has one to still go through the unbrella pulling option to do that?
> >
>
> You need distance as well as orientational restraints.  This is done with
> [intermolecular_interactions], which was a new feature in 5.1.  For
> theory, see
> dx.doi.org/10.1021/ci300505n


>
> -Justin
>

Thank you Justin, very useful help!!!

Juan José

>
> > In the case I need to do a hybrid system what would be a good procedure?
> >
> > Thank you very much.
> >
> >
> > Juan Jos? Galano Frutos
> >
> > Department of Biochemistry and
> > Molecular and Cellular Biology,
> > Faculty of Sciences,
> > University of Zaragoza
> > Pedro Cerbuna # 12, 50009
> > Zaragoza (Spain)
> > +34 976 76 28 06
> >
> > Institute for Biocomputation and
> > Physics of Complex Systems (BIFI)
> > Mariano Esquillor, Edificio I + D - 50018
> > Zaragoza (Spain)
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
>
> --
>
> Message: 4
> Date: Mon, 27 Mar 2017 12:57:36 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Regarding Glycine structure
> Message-ID: <1342227d-be3f-89b0-4f44-134a389e6...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 3/27/17 8:50 AM, Dilip H N wrote:
> > Thanks Justin,
> >
> > But my doubts are..
> > 1] after energy minimization of both glycine non zwitterionic form and
> > zwitterionic form with water, if i visualize it in vmd, the bond between
> > some of the water molecules are broken.. why is this so..??
>
> http://www.gromacs.org/Documentation/Terminology/
> Periodic_Boundary_Conditions
>
> What you see on the VMD display is its best guess as to how things are
> connected.  That's not always right.  The topology is always right.
> That's why
> trjconv exists.
>
> > 2] and ran nvt,npt,md simulations respectively...and during analysis
> part i
> > am getting only similar two types of RDF graphs...why is this
> happening...i
> > have made all the indexing, etc., proper...
> >
>
> You have provided no useful information about what these RDF plots are or
> how
> you acquired them, so there's no point for either of us in guessing.
> Maybe the
> distribution(s) that you're looking at simply don't vary as a function of
> protonation state.
>
> > Is there any tutorials for these as an example..?? solving this would
> help
> > me a lot
> >
>
> It's an amino acid in water; it's as easy of a protein system as there is.
> There's nothing special about it that requires a tutorial.
>
> -Justin
>
> >
> >    Sent with Mailtrack
> >  referral=cy16f01.di...@nitk.edu.in=22>
> >
> > On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 3/23/17 2:05 PM, Dilip H N wrote:
> >>
> >>> Hello,
> >>>
> >>> I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and
> in
> >>> the first step if i do the energy minimization and then visualizes the
> >>> mixture, the glycine is no more in its pure form as before instead it
> has
> >>> been converted to its zwitter ionic form [NH3CH2COO], and some Hydrogen
> >>> bonds with water are also broken. How can i solve these both issues..??
> >>>
> >>>
> >> Glycine didn't convert between forms.  That's impossible; bonds can't
> >> break or form in a molecular mechanical process.  The termini are
> exactly
> >> what you assigned them to be.  If you want them to be something else,
> you
> >> have to assign them as such with pdb2gmx.  Though you should note that
> NH2
> >> and COOH can't coincide at any real pH value.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> 

[gmx-users] gmx xpm2ps

[Kulkarni R]

Hi gromacs users,


After completing production run, I gave this command


gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red


However, I got error,


---
Program: gmx xpm2ps, VERSION 5.1.1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function:void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -f
File '-' does not exist or is not accessible.
The following extensions were tried to complete the file name:
  .xpm
  In command-line option -f
File 'o' does not exist or is not accessible.
The following extensions were tried to complete the file name:
  .xpm
  In command-line option -f
File name 'hbplot.eps' cannot be used for this option.
Only the following extensions are possible:
  .xpm


How to avoid this error?

What command should be given preceding to this?

How to get plot of XpixelMap file?


Thanks,

Kulkarni.R
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] FAD parameters in CHRAMm36 ff

[Amir Zeb]

Thanks Dr. Justin for your reply

On Fri, Mar 31, 2017 at 6:11 AM, Justin Lemkul  wrote:

>
>
> On 3/31/17 3:54 AM, Vytautas Rakeviius wrote:
>
>> I think you should use cgenff for FAD in such case. They are compatible
>> and can by used together.
>>
>>
> Indeed, though one should pay close attention to the parameter penalties
> in the adenine nucleotide portion of the molecule, as that part is covered
> by standard CHARMM.  Any deviations should be investigated, though they
> will probably be small and therefore unimportant.  Most of the necessary
> functional groups for FAD are already in CHARMM, just not parametrized
> explicitly, so I suspect a CGenFF topology to be of pretty high quality
> since the analogy will be strong.
>
> -Justin
>
>
>
>> On Friday, March 31, 2017 9:29 AM, Amir Zeb 
>> wrote:
>>
>>
>>  Hello Folks,
>>
>> I want to simulate a protein where FAD is included as co-factor. I will
>> use
>> CHARMm36 ff but I don't know the residue ID for FAD in this particular
>> forcefield. Anyone please let me know by which name FAD is represented in
>> CHARMm36 ff?
>>
>> Thanks in advance!
>>
>> ~Amir
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] Replica Exchange for surface tension

[Justin Lemkul]

On 3/31/17 8:13 AM, gozde ergin wrote:

Hi Justin,

I found a new optimized NBFIX parameter for SOD-Oxygen of Betaine and 
SOD-Oxygen of SDS.
On the other hand since betaine is a zwitterionic molecule there is + charge on 
Nitrogen(N) and - charge on the Oxygen atoms and SDS is anionic there is - 
charge on SO4 and there is + SOD molecules inside the bulk, I also need to 
define NBFIX parameter between N-Oxygen of betaine and N-Oxygen of SDS.
However I could not find them, do you have any hint how to develop new 
optimised NBFIX parameter these specific combination?


NBFIX parameters are used to correct overly strong/weak interactions between 
specific atom type pairs.  Generally, you need to do QM interaction energy 
calculations as a function of distance to identify the minimum energy and 
distance of that interaction.  Then compare with the stock force field values, 
and use NBFIX to correct it, if necessary.  You would not do this with full SDS 
and betaine, just some representative model compounds that contain the 
(suspected) incorrect interaction.


-Justin


There is  2016 JCTC Yoo et.al. paper that did some optimization however they 
used amine groups and betaine has tetramethylamine group.

Thanks in advance.







On 3/28/17 2:59 PM, gozde ergin wrote:

I use Charmm36 force field. Do you mean the force field parameter between
cocobetaine and SDS? Because for pure surfactant I am able to estimate the
correct surface tension. Which means force field parameter of SDS-water and
cocobetaine-water is fine.



SDS is a standard part of CHARMM36 but I have no idea what cocobetaine is.  Did 
you find existing parameters for it or did you do the parametrization yourself? 
The larger point is that you've probably stumbled upon the corner cases that 
often come up - some combination of parameters has never been looked at before 
and it requires more refinement.  If both interact with water fine but interact 
with each other improperly, that means either the SDS-cocobetaine interactions 
are too weak or too strong, or that they induce some sort of abnormal 
conformational sampling.

You'll need to look at the microscopic details of how they interact - which 
groups are associated with which, how the conformational ensembles of each 
differ from those observed in water, etc.  Then you can focus on specific 
elements of refinement that may need to be done (e.g. NBFIX for LJ interactions 
that are often the culprit in such cases, and/or perhaps some sub-par dihedral 
parameters that lead to bad sampling when a particular interaction occurs).

-Justin


Sent from my iPhone


On 28 Mar 2017, at 7:21 PM, Justin Lemkul  wrote:




On 3/28/17 12:43 PM, gozde ergin wrote: I have a mixed system of SDS and
cocobetaine on water surface. I estimated the surface tension of SDS on
water surface and cocabetaine on surface tension separately and correctly
(comparing with experimental results). However I could not estimate the
correct surface tension for SDS-cocobetaine mix in even 150 ns
simulation. Do you think replica exchange simulation would help me to
estimate the correct surface tension of mixed system? Do you have any
idea why I failed in estimating the mixed system surface tension?



If a physical model fails to produce known physical properties, the problem
is often the model itself.  I'd suspect the force field parameters first.
What is the source of your parameters?

Replica exchange helps you get over large barriers to improve sampling, but
I doubt that's useful here in a mixture of small molecules.

-Justin

-- ==

Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences School of Pharmacy Health Sciences
Facility II, Room 629 University of Maryland, Baltimore 20 Penn St.
Baltimore, MD 21201

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] Replica Exchange for surface tension

[gozde ergin]

Hi Justin,

I found a new optimized NBFIX parameter for SOD-Oxygen of Betaine and 
SOD-Oxygen of SDS. 
On the other hand since betaine is a zwitterionic molecule there is + charge on 
Nitrogen(N) and - charge on the Oxygen atoms and SDS is anionic there is - 
charge on SO4 and there is + SOD molecules inside the bulk, I also need to 
define NBFIX parameter between N-Oxygen of betaine and N-Oxygen of SDS. 
However I could not find them, do you have any hint how to develop new 
optimised NBFIX parameter these specific combination? 
There is  2016 JCTC Yoo et.al. paper that did some optimization however they 
used amine groups and betaine has tetramethylamine group.

Thanks in advance.



> 
> 
> 
> On 3/28/17 2:59 PM, gozde ergin wrote:
>> I use Charmm36 force field. Do you mean the force field parameter between
>> cocobetaine and SDS? Because for pure surfactant I am able to estimate the
>> correct surface tension. Which means force field parameter of SDS-water and
>> cocobetaine-water is fine.
>> 
> 
> SDS is a standard part of CHARMM36 but I have no idea what cocobetaine is.  
> Did you find existing parameters for it or did you do the parametrization 
> yourself? The larger point is that you've probably stumbled upon the corner 
> cases that often come up - some combination of parameters has never been 
> looked at before and it requires more refinement.  If both interact with 
> water fine but interact with each other improperly, that means either the 
> SDS-cocobetaine interactions are too weak or too strong, or that they induce 
> some sort of abnormal conformational sampling.
> 
> You'll need to look at the microscopic details of how they interact - which 
> groups are associated with which, how the conformational ensembles of each 
> differ from those observed in water, etc.  Then you can focus on specific 
> elements of refinement that may need to be done (e.g. NBFIX for LJ 
> interactions that are often the culprit in such cases, and/or perhaps some 
> sub-par dihedral parameters that lead to bad sampling when a particular 
> interaction occurs).
> 
> -Justin
> 
>> Sent from my iPhone
>> 
>>> On 28 Mar 2017, at 7:21 PM, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
 On 3/28/17 12:43 PM, gozde ergin wrote: I have a mixed system of SDS and
 cocobetaine on water surface. I estimated the surface tension of SDS on
 water surface and cocabetaine on surface tension separately and correctly
 (comparing with experimental results). However I could not estimate the
 correct surface tension for SDS-cocobetaine mix in even 150 ns
 simulation. Do you think replica exchange simulation would help me to
 estimate the correct surface tension of mixed system? Do you have any
 idea why I failed in estimating the mixed system surface tension?
 
>>> 
>>> If a physical model fails to produce known physical properties, the problem
>>> is often the model itself.  I'd suspect the force field parameters first.
>>> What is the source of your parameters?
>>> 
>>> Replica exchange helps you get over large barriers to improve sampling, but
>>> I doubt that's useful here in a mixture of small molecules.
>>> 
>>> -Justin
>>> 
>>> -- ==
>>> 
>>> Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> 
>>> Department of Pharmaceutical Sciences School of Pharmacy Health Sciences
>>> Facility II, Room 629 University of Maryland, Baltimore 20 Penn St.
>>> Baltimore, MD 21201
>>> 
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>> 
>>> == -- Gromacs Users mailing
>>> list
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> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu  
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> 
> 
> ==
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> * For 

Re: [gmx-users] Protein preparation

[Justin Lemkul]

On 3/30/17 9:59 AM, Quin K wrote:

Thank you.

There are so many pdb structures for the protein I'm looking for.
I'm not sure which one to pick.
What should I look for when picking a protein pdb structure?
I want to test for an inhibitor with the protein.
Which of the following I should look for.

Resolution
Ligands
Inhibitors attached vs Not attached.
Correct sequence of residues
Ions present
Co-factors present ? etc.



All of these things matter, and the influence of all of them are what go into 
properly conducting your research project.


-Justin


Thanks.

Regards
Quin.


On Mon, Mar 27, 2017 at 10:23 PM, Justin Lemkul  wrote:




On 3/27/17 2:16 AM, Rasika Kelum wrote:


Thank you Justin. Highly appreciate your help.

If there are missing residues, any suggestions on fixing the protein?



There are plenty of tools to do that; Modeller is one of them.

1. How to find correct sequence? (is there any website to find correct

sequence?)



This should be your first stop in starting your research.  If you don't
know the sequence or other very fundamental information, stop what you're
doing at the terminal and pull out the biology literature.

2. How to FIX the sequence (using what software?)




See above.

3. Once residues are fixed how would that affect the geometry of the

protein? Do we have to fix the geometry of protein as well?



Depends on the quality of the reconstruction of missing atoms.  Most
programs are pretty robust, but a very short energy minimization usually
relaxes away any problems.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] terminated abnormally, message of GridMAT-MD tool

[Justin Lemkul]

On 3/29/17 10:10 PM, Мижээ Батсайхан wrote:

Dear Justin,

I am using GridMAT-MD tool for analyses of heterogeneous membranes.
I generated trajectory.gro only a group which contains a peptide and
lipids.

I got following
Thread 1 terminated abnormally: Illegal division by zero at
GridMAT-MD-parallel.pl line 501.

What is the meaning of the message of the tool?



This usually means that no lipids were found in the input file, likely due to 
something incorrectly specified in the input file.


As this is not a GROMACS questions, please contact me off-list if you want to 
diagnose further.  I will need your input files (including a single frame 
coordinate file, not the whole trajectory).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] vsites with CHARMM force fields

[Erik Marklund]

On 31 Mar 2017, at 10:51, Ramon Crehuet Simon 
> wrote:

In that case, does it make sense to use virtual sites to allow 4fs time step? 
In other words, if vsites remove the fastest degrees of freedom, but we do not 
constrain bond distances, will a 4 fs time-step be stable?

No.

Kind regards,
Erik Marklund
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[gmx-users] equilibration and production run

[Neha Gupta]

Hi gromacs users,

I intend to do the following steps for protein ligand simulations (for
linear interaction energy)

(1) Energy minimization
(2) NVT equilibration (with restraints on protein  and ligand)
(3) NPT equilibration (with restraints on protein  and ligand)
(4) NPT production

During NVT and NPT equilibration run can we use brendsen method in pcoupl
and Parrinello -Rahman in production run?

Will it yield correct results?

Or should we use the same kind of pcoupl through equilibration and
production?


Thanks,
Neha
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Re: [gmx-users] FAD parameters in CHRAMm36 ff

[Vytautas Rakeviius]

I think you should use cgenff for FAD in such case. They are compatible and can 
by used together.
 

On Friday, March 31, 2017 9:29 AM, Amir Zeb  wrote:
 

 Hello Folks,

I want to simulate a protein where FAD is included as co-factor. I will use
CHARMm36 ff but I don't know the residue ID for FAD in this particular
forcefield. Anyone please let me know by which name FAD is represented in
CHARMm36 ff?

Thanks in advance!

~Amir
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[gmx-users] vsites with CHARMM force fields

[Ramon Crehuet Simon]

Dear all, 

I am simulating a system with CHARMM36m force field. Following the 
recommendations in the mailing list and the gromacs web page, I constrained 
only h-bonds (constraints = h-bonds). 

In that case, does it make sense to use virtual sites to allow 4fs time step? 
In other words, if vsites remove the fastest degrees of freedom, but we do not 
constrain bond distances, will a 4 fs time-step be stable? 

Thanks in advance, 

Ramon 
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[gmx-users] analysis of osmolyte at particular distance from backbone

[ISHRAT JAHAN]

Dear all,

I want to calculate the number of osmolyte molecule at particular distance
from backbone with respect to residue.I have tried the command trjorder but
it gives the number of osmolytes w.r.t time and i want it w.r.t residue.
Can anyone help me how to calculate this.
Thanks in advance
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Re: [gmx-users] Pdb2gmx

[Saumyak Mukherjee]

Dear Lamm,

It is GROMACS-5.0.7. So you need to use "gmx pdb2gmx" command.

Best Wishes,
Saumyak

On 31 March 2017 at 11:55, Lamm Gro  wrote:

> Dear Gromacs users ,
>
> I have installed Gromacs by this way :
> http://www.gromacs.org/Documentation/Installation_
> Instructions_5.0#quick-and-dirty-installation
>
>
> every thing was fine and I could install the package completely .
> But now I can't find pdb2gmx command !
> Can you please let me know what the problem is ?
> I have updated cmake and fftw !
>
> Best,
> Saeed.
> --
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>



-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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[gmx-users] calculating gbsa parameters for metal ion

[Javaria ashraf]

Hello and greetingsi am simulating my protein in implicit solvent. the protein 
has ca2+ ion in it. the gbsa.itp file doesn't have parameters for any ion.how 
can i add parameters of my ion?As mentioned in tutorial.[ 
implicit_genborn_params ];Atomtype sar st pi gbr hct
Values in columns 1-3 are not currently used. Column 4 contains the atomic van 
der Waals radii, which are used in computing the Born radii. 
the van der Waals radii of ca2+ is 0.231? is it right? or how can i calculate 
the hct?thank you
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[gmx-users] FAD parameters in CHRAMm36 ff

[Amir Zeb]

Hello Folks,

I want to simulate a protein where FAD is included as co-factor. I will use
CHARMm36 ff but I don't know the residue ID for FAD in this particular
forcefield. Anyone please let me know by which name FAD is represented in
CHARMm36 ff?

Thanks in advance!

~Amir
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[gmx-users] Pdb2gmx

[Lamm Gro]

Dear Gromacs users ,

I have installed Gromacs by this way :
http://www.gromacs.org/Documentation/Installation_Instructions_5.0#quick-and-dirty-installation


every thing was fine and I could install the package completely .
But now I can't find pdb2gmx command !
Can you please let me know what the problem is ?
I have updated cmake and fftw !

Best,
Saeed.
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Re: [gmx-users] MMPBSA analysis on GROMACS trajectory

[Neha Gupta]

Thank you for the reply.

I am using cygwin64 for my computations.

Had already tried the above mentioned link.

It is not working in CYGWIN64.

Thanks,
Neha



On Mon, Mar 27, 2017 at 1:07 PM, masoud keramati 
wrote:

> Hi
> They have a web site and all of things you need is there:
> http://rashmikumari.github.io/g_mmpbsa/
>
> On Mar 27, 2017 10:15 AM, "Neha Gupta"  wrote:
>
> > Hi gromacs users,
> >
> > How to calculate MMPBSA analysis on Gromacs trajectory using MMPBSA tool
> of
> > amber software package?
> >
> >
> > Thanks,
> > Neha
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