[gmx-users] error with indexfile

[Kieu Thu Nguyen]

Dear All,

When using the command
grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o
equilibrate.tpr
The error is
Fatal error:
Invalid atom number 6518 in indexfile
How can i fix this ?
Thank so much for any help !
Regards,
KT
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Re: [gmx-users] Unusual processing time

[Justin Lemkul]

On 1/3/13 9:39 PM, Xu Dong Huang wrote:

The average of all my variations contain about 802780 atoms.



The general rule of thumb is to aim for a few hundred or maybe a thousand atoms 
per processor.  Given that you have in excess of 130,000 atoms per processor, I 
would say your observation of slow performance is entirely normal.


-Justin



Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu

On Jan 3, 2013, at 9:36 PM, Justin Lemkul  wrote:




On 1/3/13 9:33 PM, Xu Dong Huang wrote:

Actually, I correct myself, it's not even a 85x85x85 system, it's a 45x45x45 
box system with water solvent + large multiple solutes.



Performance depends mostly on the number of atoms.  You haven't provided that 
information, so it's hard to judge what you might expect.

-Justin


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu

On Jan 3, 2013, at 9:29 PM, Xu Dong Huang  wrote:


Dear gromac users,

I submitted my NPT run into a MPI cluster. The size of my run system is an 
85x85x85 box filled with water solvent. and I set NPT steps to be 100 
(1million) with dt 0.02. The log says It will finish sometime in mid or towards 
end of february.

Is that normal for a NPT run of that size? Or am I just faced with slow 
technology. Or am I doing something wrong (I requested 6 cores for my run)
Please let me know, thanks.

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu

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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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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] Unusual processing time

[Xu Dong Huang]

The average of all my variations contain about 802780 atoms. 


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudo...@eden.rutgers.edu 

On Jan 3, 2013, at 9:36 PM, Justin Lemkul  wrote:

> 
> 
> On 1/3/13 9:33 PM, Xu Dong Huang wrote:
>> Actually, I correct myself, it's not even a 85x85x85 system, it's a 45x45x45 
>> box system with water solvent + large multiple solutes.
>> 
> 
> Performance depends mostly on the number of atoms.  You haven't provided that 
> information, so it's hard to judge what you might expect.
> 
> -Justin
> 
>> Xu Dong Huang
>> Chemical & Biochemical Engineering
>> Rutgers School of Engineering
>> xudo...@eden.rutgers.edu
>> 
>> On Jan 3, 2013, at 9:29 PM, Xu Dong Huang  wrote:
>> 
>>> Dear gromac users,
>>> 
>>> I submitted my NPT run into a MPI cluster. The size of my run system is an 
>>> 85x85x85 box filled with water solvent. and I set NPT steps to be 100 
>>> (1million) with dt 0.02. The log says It will finish sometime in mid or 
>>> towards end of february.
>>> 
>>> Is that normal for a NPT run of that size? Or am I just faced with slow 
>>> technology. Or am I doing something wrong (I requested 6 cores for my run)
>>> Please let me know, thanks.
>>> 
>>> Xu Dong Huang
>>> Chemical & Biochemical Engineering
>>> Rutgers School of Engineering
>>> xudo...@eden.rutgers.edu
>>> 
>>> --
>>> 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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>> 
> 
> -- 
> 
> 
> 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] Unusual processing time

[Justin Lemkul]

On 1/3/13 9:33 PM, Xu Dong Huang wrote:

Actually, I correct myself, it's not even a 85x85x85 system, it's a 45x45x45 
box system with water solvent + large multiple solutes.



Performance depends mostly on the number of atoms.  You haven't provided that 
information, so it's hard to judge what you might expect.


-Justin


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu

On Jan 3, 2013, at 9:29 PM, Xu Dong Huang  wrote:


Dear gromac users,

I submitted my NPT run into a MPI cluster. The size of my run system is an 
85x85x85 box filled with water solvent. and I set NPT steps to be 100 
(1million) with dt 0.02. The log says It will finish sometime in mid or towards 
end of february.

Is that normal for a NPT run of that size? Or am I just faced with slow 
technology. Or am I doing something wrong (I requested 6 cores for my run)
Please let me know, thanks.

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu

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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] Unusual processing time

[Xu Dong Huang]

Actually, I correct myself, it's not even a 85x85x85 system, it's a 45x45x45 
box system with water solvent + large multiple solutes. 

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudo...@eden.rutgers.edu 

On Jan 3, 2013, at 9:29 PM, Xu Dong Huang  wrote:

> Dear gromac users,
> 
> I submitted my NPT run into a MPI cluster. The size of my run system is an 
> 85x85x85 box filled with water solvent. and I set NPT steps to be 100 
> (1million) with dt 0.02. The log says It will finish sometime in mid or 
> towards end of february. 
> 
> Is that normal for a NPT run of that size? Or am I just faced with slow 
> technology. Or am I doing something wrong (I requested 6 cores for my run) 
> Please let me know, thanks. 
> 
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering 
> xudo...@eden.rutgers.edu 
> 
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[gmx-users] Unusual processing time

[Xu Dong Huang]

Dear gromac users,

I submitted my NPT run into a MPI cluster. The size of my run system is an 
85x85x85 box filled with water solvent. and I set NPT steps to be 100 
(1million) with dt 0.02. The log says It will finish sometime in mid or towards 
end of february. 

Is that normal for a NPT run of that size? Or am I just faced with slow 
technology. Or am I doing something wrong (I requested 6 cores for my run) 
Please let me know, thanks. 

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudo...@eden.rutgers.edu 

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Re: [gmx-users] Question about gold-S simulation

[Justin Lemkul]

On 1/3/13 3:49 PM, hyunj...@andrew.cmu.edu wrote:

Hi,

I saw Fatemeh's and others' posts regarding gold and S FF parameters.
I have a few questions regarding this:

1. The vdW parameters for Au changed according to interaction atoms such
as C, H, N, S, etc.
However, I wonder, if the system includes both S and N, which interact
with Au, then which parameter should I use for Au, one for Au-N or one for
Au-S.



LJ parameters listed in [atomtypes] in ffnonbonded.itp are used in conjunction 
with the combination rules of the force field to determine these interactions. 
If interactions change depending upon the atoms involved, one can specify 
[nonbond_params] for each interaction pair that supersede the combination rules 
for those atom pairs.  That way, the parameters for e.g. S can be different when 
interacting with different atoms.


I can't comment on points 2 and 3.

-Justin



2. Can you send me papers you obtained the FF parameters for Au?


3. The charge of Au is zero?

Thanks in advance.

Hyunjin.





--


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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[gmx-users] Question about gold-S simulation

[hyunjink]

Hi,

I saw Fatemeh's and others' posts regarding gold and S FF parameters.
I have a few questions regarding this:

1. The vdW parameters for Au changed according to interaction atoms such
as C, H, N, S, etc.
However, I wonder, if the system includes both S and N, which interact
with Au, then which parameter should I use for Au, one for Au-N or one for
Au-S.


2. Can you send me papers you obtained the FF parameters for Au?


3. The charge of Au is zero?

Thanks in advance.

Hyunjin.



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Re: [gmx-users] Re: Simulation of 2D lattice model

[Justin Lemkul]

On 1/3/13 2:01 PM, James Starlight wrote:

Justin,

thanks again for explanation. By the way if I define in topology top
LJ params like

; Include forcefield parameters
#include "gromos53a5.ff/forcefield.itp"

[ atomtypes ]
;name  at.num   mass  charge ptype   c6   c12
   CH26 0.000  0.000 A  0.0074684164  3.3965584e-05
   CH36 0.000  0.000 A  0.0096138025  2.6646244e-05

[ nonbond_params ]
; ij func  c6   c12
  CH3  CH2  1  0.008473481  3.0084136e-05

[ moleculetype ]
; Namenrexcl
ICE 3

i've obtain warns

WARNING 1 [file lattice.top, line 23]:
   Overriding atomtype CH2


WARNING 2 [file lattice.top, line 24]:
   Overriding atomtype CH3

does it mean that the params from topology.top will be used instead of
RTP file ?



Not from the .rtp file, but the .top is overriding the contents of 
ffnonbonded.itp.

-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] Re: Simulation of 2D lattice model

[James Starlight]

Justin,

thanks again for explanation. By the way if I define in topology top
LJ params like

; Include forcefield parameters
#include "gromos53a5.ff/forcefield.itp"

[ atomtypes ]
;name  at.num   mass  charge ptype   c6   c12
  CH26  0.000  0.000 A  0.0074684164  3.3965584e-05
  CH36  0.000  0.000 A  0.0096138025  2.6646244e-05

[ nonbond_params ]
; ij func  c6   c12
 CH3  CH2  1  0.008473481  3.0084136e-05

[ moleculetype ]
; Namenrexcl
ICE 3

i've obtain warns

WARNING 1 [file lattice.top, line 23]:
  Overriding atomtype CH2


WARNING 2 [file lattice.top, line 24]:
  Overriding atomtype CH3

does it mean that the params from topology.top will be used instead of
RTP file ?

James

2013/1/3, Justin Lemkul :
>
>
> On 1/3/13 11:49 AM, James Starlight wrote:
>> Justin,
>>
>>
>> I've made new lattice model in GROMOS united atoms. I've used 2 nodes
>> - CH2 (ca) for atom with 3 bonds as well as CH1 (CB) for boundary
>> atoms with 2 bonds to adjacent nodes.
>
> I'm assuming you've simply switched the atom types here.  A CH2 should not
> have
> 3 other bonds.
>
>> That system is considerably rigid in comparison to the lattice which
>> I've simulated in OPLS all atom ff.
>>
>> Does it possible to change VDW(LJ) parameters for both nodes in the
>> top file or should I modify existing atom types in ffnonbonded ?
>>
>
> You can do anything you like, but you'd better have good justification for
> it.
> Making ad hoc changes to force fields that were not necessarily designed to
> do
> what you think it should is generally very unwise.  Whatever you do, make
> changes in a local copy of the force field so you don't screw up other
> simulations later on, or even better, make a special [atomtypes] directive
> in
> your .top file.
>
>> How I could prevent rotation of the lattice as the whole object ? (
>> simulation in vacuum in NVT) without any posres ?
>
> I can't think of a way to do this, nor would it have any real functional
> purpose.  You can remove rotation and translation afterwards with trjconv.
>
>> Its not possible to use very small box dimensions due to the rvdv= 1.4
>> in gromos ff
>> (if I define box vectors compatible with the size of the lattice I've
>> obtain error in grompp)
>
> If you're running in vacuo, you should turn off PBC and use infinite
> cutoffs,
> otherwise you likely will have periodicity artifacts and you are not truly
> simulating in vacuo.
>
>>
>> Also in connection to the above question with the box size I also
>> wounder like to know how I could use ; periodic_molecules  options
>> with such lattice which asymmetric on left and right boundaries (
>> picture http://imageshack.us/photo/my-images/543/lattice.png/ ) ?
>>
>
> Some boxes have hexagonal cross-sections (see the manual) that might be
> useful.
>   In a basic sense, all you need to have is atoms that should be bonded to
> one
> another through a periodic boundary should be separated by one bond length
> (i.e.
> half a bond length on either side of the box) and make sure these bonds are
>
> added to the topology (probably by hand).  Then the periodic_molecules
> option
> works its magic and you have an infinite lattice.
>
> -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] Re: Simulation of 2D lattice model

[Justin Lemkul]

On 1/3/13 11:49 AM, James Starlight wrote:

Justin,


I've made new lattice model in GROMOS united atoms. I've used 2 nodes
- CH2 (ca) for atom with 3 bonds as well as CH1 (CB) for boundary
atoms with 2 bonds to adjacent nodes.


I'm assuming you've simply switched the atom types here.  A CH2 should not have 
3 other bonds.



That system is considerably rigid in comparison to the lattice which
I've simulated in OPLS all atom ff.

Does it possible to change VDW(LJ) parameters for both nodes in the
top file or should I modify existing atom types in ffnonbonded ?



You can do anything you like, but you'd better have good justification for it. 
Making ad hoc changes to force fields that were not necessarily designed to do 
what you think it should is generally very unwise.  Whatever you do, make 
changes in a local copy of the force field so you don't screw up other 
simulations later on, or even better, make a special [atomtypes] directive in 
your .top file.



How I could prevent rotation of the lattice as the whole object ? (
simulation in vacuum in NVT) without any posres ?


I can't think of a way to do this, nor would it have any real functional 
purpose.  You can remove rotation and translation afterwards with trjconv.



Its not possible to use very small box dimensions due to the rvdv= 1.4
in gromos ff
(if I define box vectors compatible with the size of the lattice I've
obtain error in grompp)


If you're running in vacuo, you should turn off PBC and use infinite cutoffs, 
otherwise you likely will have periodicity artifacts and you are not truly 
simulating in vacuo.




Also in connection to the above question with the box size I also
wounder like to know how I could use ; periodic_molecules  options
with such lattice which asymmetric on left and right boundaries (
picture http://imageshack.us/photo/my-images/543/lattice.png/ ) ?



Some boxes have hexagonal cross-sections (see the manual) that might be useful. 
 In a basic sense, all you need to have is atoms that should be bonded to one 
another through a periodic boundary should be separated by one bond length (i.e. 
half a bond length on either side of the box) and make sure these bonds are 
added to the topology (probably by hand).  Then the periodic_molecules option 
works its magic and you have an infinite lattice.


-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] Re: Simulation of 2D lattice model

[James Starlight]

Justin,


I've made new lattice model in GROMOS united atoms. I've used 2 nodes
- CH2 (ca) for atom with 3 bonds as well as CH1 (CB) for boundary
atoms with 2 bonds to adjacent nodes.
That system is considerably rigid in comparison to the lattice which
I've simulated in OPLS all atom ff.

Does it possible to change VDW(LJ) parameters for both nodes in the
top file or should I modify existing atom types in ffnonbonded ?

How I could prevent rotation of the lattice as the whole object ? (
simulation in vacuum in NVT) without any posres ?
Its not possible to use very small box dimensions due to the rvdv= 1.4
in gromos ff
(if I define box vectors compatible with the size of the lattice I've
obtain error in grompp)

Also in connection to the above question with the box size I also
wounder like to know how I could use ; periodic_molecules  options
with such lattice which asymmetric on left and right boundaries (
picture http://imageshack.us/photo/my-images/543/lattice.png/ ) ?


Thanks for help

James

2013/1/3, Justin Lemkul :
>
>
> On 1/3/13 7:25 AM, James Starlight wrote:
>> Justin,
>>
>> yes, the main task is the parametrization of the simple 2D lattice
>> which I created from sp3 carbons as the nodes. Now the main task is
>> the reducing of that model  to simplest 2D lattice made from 1 type of
>> any atom connected with the 3 adjacent nodes via flexible bonds.
>>
>> Might I define new atom type for that node   in the atomname2type.n2t
>> file placed to the work dir or should I add that atom to the ffbonded
>> of the opls or gromos ff ?
>>
>
> You can't define atomtypes in .n2t files; they can only make use of existing
>
> types.  You need to modify ffnonbonded.itp, not ffbonded.itp in that case.
> I
> still don't see why you would need a new type; this would only be required
> to
> introduce new LJ parameters.  You can use existing united-atom types and
> define
> as many bonds to them as you want (regardless of whether or not they make
> chemical sense) in the .n2t file.
>
> -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] gromacs demo

[Felipe Pineda, PhD]

Maybe you can try first another tutorials, eg.

http://manuals.bioinformatics.ucr.edu/home/linux-basics

On 01/03/2013 03:16 PM, amna khan wrote:

the command
/usr/share/gromacs/tutor/gmxdemo/demo

no such cooamnd found...

cd  /usr/share/gromacs/tutor/gmxdemo/demo

permsion denied

sudo /usr/share/gromacs/tutor/gmxdemo/demo

comand not found

i am not getting any results



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Re: [gmx-users] gromacs demo

[Justin Lemkul]

On 1/3/13 9:16 AM, amna khan wrote:

the command
/usr/share/gromacs/tutor/gmxdemo/demo

no such cooamnd found...

cd  /usr/share/gromacs/tutor/gmxdemo/demo

permsion denied



You can't cd into a script.


sudo /usr/share/gromacs/tutor/gmxdemo/demo

comand not found

i am not getting any results



It seems like Gromacs is installed somewhere else or has restrictive permissions 
that prohibit you from accessing it.  Like I said, better tutorial material 
exists and would probably be a better use of time.


-Justin





On Thu, Jan 3, 2013 at 4:19 PM, Justin Lemkul  wrote:




On 1/3/13 6:06 AM, amna khan wrote:


hi all.

i am a beginer user of ubuntu and gromacs
i installed gormacs on ubuntu 12.10 and now want to run demo , i dont know
how to run this correctly

i do by typing cd /usr/share/gromacs/tutor/**gmxdemo

it gives nothing as output



You changed into a directory; you didn't actually run anything.  There's a
script called 'demo' in that directory that you need to execute to get it
to run.




help me please in running the demo



The demo is significantly less useful than the many tutorials provided
online.

http://www.gromacs.org/**Documentation/Tutorials

-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] gromacs demo

[amna khan]

the command
/usr/share/gromacs/tutor/gmxdemo/demo

no such cooamnd found...

cd  /usr/share/gromacs/tutor/gmxdemo/demo

permsion denied

sudo /usr/share/gromacs/tutor/gmxdemo/demo

comand not found

i am not getting any results




On Thu, Jan 3, 2013 at 4:19 PM, Justin Lemkul  wrote:

>
>
> On 1/3/13 6:06 AM, amna khan wrote:
>
>> hi all.
>>
>> i am a beginer user of ubuntu and gromacs
>> i installed gormacs on ubuntu 12.10 and now want to run demo , i dont know
>> how to run this correctly
>>
>> i do by typing cd /usr/share/gromacs/tutor/**gmxdemo
>>
>> it gives nothing as output
>>
>>
> You changed into a directory; you didn't actually run anything.  There's a
> script called 'demo' in that directory that you need to execute to get it
> to run.
>
>
>
>> help me please in running the demo
>>
>>
> The demo is significantly less useful than the many tutorials provided
> online.
>
> http://www.gromacs.org/**Documentation/Tutorials
>
> -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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> 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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Re: [gmx-users] problem by start with grompp

[Alexej Mazheika]

Thank you

On Thu, Jan 3, 2013 at 2:39 PM, Justin Lemkul  wrote:

> spc216.gro
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Re: [gmx-users] problem by start with grompp

[Justin Lemkul]

On 1/3/13 7:34 AM, Alexej Mazheika wrote:

Dear all!

I'm new with Gromacs.
I prepared some job for it but I cann't start with grompp. It writes me
"Fatal error:
Something is wrong in the coordinate formatting of file conf.gro. Note that
gro is fixed format (see the manual)".
What is wrong? I want to calculate a silver cluster contining 125 atoms.
And the conf.gro file was prepared according to on-line manual of Gromacs.
Input-files (conf.gro, topol.top and silver.itp) are shown below.

Thank you in advance,
Alex

*conf.gro:*

Bulk silver, t = 0.0
  125
 ClusterAg10.0000.0000.0000.35490.4758
-0.0904


Immediately you can see that the format is wrong.  First comes a residue number 
(5 characters, right-aligned), then a residue name (also 5 characters max). 
Your file satisfies neither requirement, as you have no residue number and a 
7-character residue name.  Email format makes it somewhat hard to judge the 
remainder of the file, but at a glance, it appears the spacing is misaligned for 
all columns.  Refer again to the online manual and compare your format against 
existing examples (like spc216.gro in $GMXLIB).


-Justin


 ClusterAg20.2040.2040.0000.50230.6171
-0.1193
 ClusterAg30.4090.4090.0000.17061.9242
-0.1299
 ClusterAg4-0.409-0.4090.0000.1853-0.0977
0.2463
 ClusterAg5-0.204-0.2040.000-0.1168
-0.03710.9161
 ClusterAg60.2040.0000.204-0.05511.4850
-0.1296
 ClusterAg70.4090.2040.2040.3101-0.3484
-0.0008
 ClusterAg80.6130.4090.2040.52980.4809
0.2331
 ClusterAg9-0.204-0.4090.204-0.4401
-0.39461.5223
 ClusterAg100.000-0.2040.204-0.0845
-0.0352-0.6628
 ClusterAg110.4090.0000.409-0.54230.5471
-0.3902
 ClusterAg120.6130.2040.409-3.12800.3170
-1.0229
 ClusterAg130.8170.4090.4090.67890.0640
-0.0344
 ClusterAg140.000-0.4090.409-0.13020.1578
-0.0127
 ClusterAg150.204-0.2040.4090.66981.0679
-1.3227
 ClusterAg16-0.4090.000-0.409-0.2256
-0.36320.0514
 ClusterAg17-0.2040.204-0.4090.2069
-0.23880.6106
 ClusterAg180.0000.409-0.4090.73491.3763
-0.9274
 ClusterAg19-0.817-0.409-0.409-0.9525
-0.26270.4172
 ClusterAg20-0.613-0.204-0.4090.5542
-0.4907-0.0019
 ClusterAg21-0.2040.000-0.2041.27321.4340
-0.3768
 ClusterAg220.0000.204-0.2040.0591-0.1353
-0.5894
 ClusterAg230.2040.409-0.204-0.5937
-0.17210.0862
 ClusterAg24-0.613-0.409-0.2040.4257
2.10610.2350
 ClusterAg25-0.409-0.204-0.2040.2298
-0.07750.3642
 ClusterAg260.0000.2040.204-0.03840.0506
-0.0643
 ClusterAg270.2040.4090.204-1.22602.3805
-0.4377
 ClusterAg280.4090.6130.2040.3871-0.0963
-0.0275
 ClusterAg29-0.409-0.2040.2040.3262
-0.1153-0.1338
 ClusterAg30-0.2040.0000.2040.9592-0.5738
-0.0823
 ClusterAg310.2040.2040.4090.54130.4476
-0.0550
 ClusterAg320.4090.4090.409-0.3161-0.2168
-0.1527
 ClusterAg330.6130.6130.409-0.68140.5993
-0.2307
 ClusterAg34-0.204-0.2040.4090.25520.4818
-0.0729
 ClusterAg350.0000.0000.4090.04080.0414
-0.0155
 ClusterAg360.4090.2040.613-0.8836-0.7443
0.2603
 ClusterAg370.6130.4090.613-0.2645-0.3151
-0.2842
 ClusterAg380.8170.6130.613-0.2692-0.2904
-0.2710
 ClusterAg390.000-0.2040.6130.7939-0.8404
0.2681
 ClusterAg400.2040.0000.613-0.9573-0.0950
-0.1476
 ClusterAg41-0.4090.204-0.204-0.0251
0.14130.8754
 ClusterAg42-0.2040.409-0.2040.26092.5060
-0.0260
 ClusterAg430.0000.613-0.2040.0891-0.0179
-0.5820
 ClusterAg44-0.817-0.204-0.2040.0411
-0.1423-0.0371
 ClusterAg45-0.6130.000-0.2042.3046
-0.1273-0.3149
 ClusterAg46-0.2040.2040.0000.14410.1891
0.4334
 ClusterAg470.0000.4090.0000.1110-0.0916
-0.3021
 ClusterAg480.2040.6130.0001.77410.8838

Re: [gmx-users] Re: Simulation of 2D lattice model

[Justin Lemkul]

On 1/3/13 7:25 AM, James Starlight wrote:

Justin,

yes, the main task is the parametrization of the simple 2D lattice
which I created from sp3 carbons as the nodes. Now the main task is
the reducing of that model  to simplest 2D lattice made from 1 type of
any atom connected with the 3 adjacent nodes via flexible bonds.

Might I define new atom type for that node   in the atomname2type.n2t
file placed to the work dir or should I add that atom to the ffbonded
of the opls or gromos ff ?



You can't define atomtypes in .n2t files; they can only make use of existing 
types.  You need to modify ffnonbonded.itp, not ffbonded.itp in that case.  I 
still don't see why you would need a new type; this would only be required to 
introduce new LJ parameters.  You can use existing united-atom types and define 
as many bonds to them as you want (regardless of whether or not they make 
chemical sense) in the .n2t file.


-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] problem by start with grompp

[Justin Lemkul]

On 1/3/13 7:23 AM, Alexej Mazheika wrote:

Dear all!

I'm new with Gromacs.
I prepared some job for it but I cann't start with grompp. It writes me
"Fatal error:
Something is wrong in the coordinate formatting of file conf.gro. Note that
gro is fixed format (see the manual)".
What is wrong? I want to calculate a silver cluster contining 125 atoms.
And the conf.gro file was prepared according to on-line manual of Gromacs.
Corresponding input-files are attached here.



The mailing list does not accept attachments.  Please cut and paste into the 
message body.


-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] coordinates obtained from the Automated Topology Builder

[Justin Lemkul]

On 1/3/13 7:11 AM, Ahmet yıldırım wrote:

Dear users,

I get topology (A.itp) and structure (A.gro) files of a ligand using
Automated Topology Builder.
A.gro file has optimised geometry. That is, the coordinates of the
atoms have been changed according to the initial file .pdb.
I am confused. When I do simulation related to protein-ligand
interactions, which coordinates I use?
Optimised coordinates obtained from the Automated Topology Builder or
original coordinates in .pdb?



If you have a ligand in complex with a protein, and then an optimization is done 
in the absence of the restricting influence of the protein, you'll probably get 
very bad interactions.  Always use the original coordinates in these cases.


-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] Re: Simulation of 2D lattice model

[James Starlight]

Justin,

yes, the main task is the parametrization of the simple 2D lattice
which I created from sp3 carbons as the nodes. Now the main task is
the reducing of that model  to simplest 2D lattice made from 1 type of
any atom connected with the 3 adjacent nodes via flexible bonds.

Might I define new atom type for that node   in the atomname2type.n2t
file placed to the work dir or should I add that atom to the ffbonded
of the opls or gromos ff ?

James

2013/1/3, Justin Lemkul :
>
>
> On 1/3/13 2:46 AM, James Starlight wrote:
>> Justin,
>>
>>   I want to simulate lattice with flexible nodes ( to examine
>> fluctuations of that system by mens of Normal Mode Analysis). If I
>> choose sp3 carbons as the nodes I obtain such lattice. But In that
>> system hydrogens are also present which are not desirable in my system
>> ( i want system consisted of only one type of atoms). On contrary if I
>> choose sp2 hydrogens as the nodes I obtain completely rigid lattice
>> which are not suitable for me.
>>
>
> OK, so all the talk of a 2D lattice and issues assigning impropers really
> wasn't
> what you wanted after all?  This whole thread has gotten to be very
> meandering
> and contradictory, I'm sorry to say.  Only now after several days of posts
> do
> your real goals come out.
>
>> I suppose that united-atom model could be suitable for such flexible
>> lattice but I've failed to apply g_x2top  on my lattice with gromos
>> force field ( I have no problems with the opls-aa for this system).
>>
>> Here I've obtain errors like
>>
>> Can not find forcefield for atom C116-70 with 3 bonds
>> Can not find forcefield for atom C119-71 with 3 bonds
>> Can not find forcefield for atom C120-72 with 3 bonds
>> Can not find forcefield for atom C121-73 with 3 bonds
>> Can not find forcefield for atom C122-74 with 3 bonds
>> Can not find forcefield for atom C124-75 with 3 bonds
>> Can not find forcefield for atom C125-76 with 3 bonds
>> Can not find forcefield for atom C126-77 with 3 bonds
>> Can not find forcefield for atom C127-78 with 3 bonds
>> Can not find forcefield for atom H01-79 with 0 bonds
>> Can not find forcefield for atom H02-80 with 0 bonds
>> Can not find forcefield for atom H03-81 with 0 bonds
>> Can not find forcefield for atom H04-82 with 0 bonds
>> Can not find forcefield for atom H05-83 with 0 bonds
>>
>> So it seems that the bonds  between C and H atoms were not recognized
>> correclty in case of gromos-ff. Must the some corrections be done in
>> the atomname2type.n2t file ?
>>
>
> There are no explicit hydrogens in any of the Gromos force fields for atoms
> like
> these (hence "united atom"), and IIRC there are no .n2t files for any of
> them.
> So it's not a matter of changing an .n2t file, it's a matter of creating
> one.
>
> -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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[gmx-users] coordinates obtained from the Automated Topology Builder

[Ahmet yıldırım]

Dear users,

I get topology (A.itp) and structure (A.gro) files of a ligand using
Automated Topology Builder.
A.gro file has optimised geometry. That is, the coordinates of the
atoms have been changed according to the initial file .pdb.
I am confused. When I do simulation related to protein-ligand
interactions, which coordinates I use?
Optimised coordinates obtained from the Automated Topology Builder or
original coordinates in .pdb?

Thanks in advance
--
Ahmet Yıldırım
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Re: [gmx-users] Re: g_saltbr not include side chains of GLU and ASP??

[Kavyashree M]

Sir,

I used OPLS-AA ff. Thank you very mush for your effort.
Its clear now. AS you said It assigns the number of the 1st
atom of the charge group in the output file.

Thank you
kavya

On Thu, Jan 3, 2013 at 5:01 PM, Justin Lemkul  wrote:

>
>
> On 1/3/13 5:15 AM, Kavyashree M wrote:
>
>> Dear users,
>>
>> I would like to add that in case of ARG or LYS, the sidechain
>> nitrogen atoms (NE,NZ,NH1,NH2) are present in the output.
>> The problem s only with GLU and ASP residues.
>> I use 4.5.3 version
>>
>>
> I only took a quick look through the code, but it seems that what g_saltbr
> is doing is labeling its output files based on the first atom in a given
> charge group.  The charge group, not the individual atoms per se, are what
> dictate the search criteria.  You haven't said which force field you're
> using, but I will assume it's one of the Gromos ones, wherein the C[GD]
> atom is the first atom in the COO- charge group.
>
> -Justin
>
>
>  Thank you
>> kavya
>>
>> On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M  wrote:
>>
>>  Dear users,
>>>
>>> I used g_saltbr to calculate the salt-bridge interactions using:
>>> g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep
>>> It gave the output for each atom-atom interaction within
>>> the given cut-off.
>>> When I checked the atom type that corresponds to the atom
>>> number output in each file, side chain oxygen atoms of ASP
>>> and GLU was not present in any of  the file. And most of the
>>> atoms that corresponds to the ASP and GLU were CB, CG or
>>> CD.
>>> Kindly someone clarify why is this so.
>>>
>>> Thank you
>>> Kavya
>>>
>>>
> --
> ==**==
>
> 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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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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Re: [gmx-users] Re: g_saltbr not include side chains of GLU and ASP??

[Justin Lemkul]

On 1/3/13 5:15 AM, Kavyashree M wrote:

Dear users,

I would like to add that in case of ARG or LYS, the sidechain
nitrogen atoms (NE,NZ,NH1,NH2) are present in the output.
The problem s only with GLU and ASP residues.
I use 4.5.3 version



I only took a quick look through the code, but it seems that what g_saltbr is 
doing is labeling its output files based on the first atom in a given charge 
group.  The charge group, not the individual atoms per se, are what dictate the 
search criteria.  You haven't said which force field you're using, but I will 
assume it's one of the Gromos ones, wherein the C[GD] atom is the first atom in 
the COO- charge group.


-Justin


Thank you
kavya

On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M  wrote:


Dear users,

I used g_saltbr to calculate the salt-bridge interactions using:
g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep
It gave the output for each atom-atom interaction within
the given cut-off.
When I checked the atom type that corresponds to the atom
number output in each file, side chain oxygen atoms of ASP
and GLU was not present in any of  the file. And most of the
atoms that corresponds to the ASP and GLU were CB, CG or
CD.
Kindly someone clarify why is this so.

Thank you
Kavya



--


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: Fw: [gmx-users] Amidated C-terminal

[Shima Arasteh]

Thanks for your kind reply.
Maybe I made a mistake unintentionally in modification of files. The CT2 in 
charmm folder I downloaded from the source, is the same as you wrote.
Thanks.


 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Thursday, January 3, 2013 2:47 PM
Subject: Re: Fw: [gmx-users] Amidated C-terminal



On 1/3/13 6:11 AM, Shima Arasteh wrote:
> Have a look at CT2 in aminoacids.c.tdb please:
> 
> [ CT2 ]
> [ replace ]
>   O        CC        12.011    0.55
>   O        O        15.9994    -0.55
> 
> 
> It is +0.55 as what you said. But I see all carbonyl C in aminoacids.rtp file 
> have +0.51 charge.
> I think the amidated C-terminal in my top file should be charged +0.55 as 
> what I see in c.tdb. Shouldn't be? Why it couldn't understand to take +0.55 
> charge for this last residue?
> 

There is an error in the .tdb file.  The first [replace] line attempts to 
replace an O atom and assign it a CC type with charge of +0.55, which is then 
overridden by the next line, which assigns the O atom an O type with -0.55 
charge.  The carbonyl C is (erroneously) not adjusted.  The correct line is 
present in the charmm27.ff folder:

[ CT2 ]
[ replace ]
C      CC      12.011  0.55
O      O       15.9994 -0.55

-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] Re: Simulation of 2D lattice model

[Justin Lemkul]

On 1/3/13 2:46 AM, James Starlight wrote:

Justin,

  I want to simulate lattice with flexible nodes ( to examine
fluctuations of that system by mens of Normal Mode Analysis). If I
choose sp3 carbons as the nodes I obtain such lattice. But In that
system hydrogens are also present which are not desirable in my system
( i want system consisted of only one type of atoms). On contrary if I
choose sp2 hydrogens as the nodes I obtain completely rigid lattice
which are not suitable for me.



OK, so all the talk of a 2D lattice and issues assigning impropers really wasn't 
what you wanted after all?  This whole thread has gotten to be very meandering 
and contradictory, I'm sorry to say.  Only now after several days of posts do 
your real goals come out.



I suppose that united-atom model could be suitable for such flexible
lattice but I've failed to apply g_x2top  on my lattice with gromos
force field ( I have no problems with the opls-aa for this system).

Here I've obtain errors like

Can not find forcefield for atom C116-70 with 3 bonds
Can not find forcefield for atom C119-71 with 3 bonds
Can not find forcefield for atom C120-72 with 3 bonds
Can not find forcefield for atom C121-73 with 3 bonds
Can not find forcefield for atom C122-74 with 3 bonds
Can not find forcefield for atom C124-75 with 3 bonds
Can not find forcefield for atom C125-76 with 3 bonds
Can not find forcefield for atom C126-77 with 3 bonds
Can not find forcefield for atom C127-78 with 3 bonds
Can not find forcefield for atom H01-79 with 0 bonds
Can not find forcefield for atom H02-80 with 0 bonds
Can not find forcefield for atom H03-81 with 0 bonds
Can not find forcefield for atom H04-82 with 0 bonds
Can not find forcefield for atom H05-83 with 0 bonds

So it seems that the bonds  between C and H atoms were not recognized
correclty in case of gromos-ff. Must the some corrections be done in
the atomname2type.n2t file ?



There are no explicit hydrogens in any of the Gromos force fields for atoms like 
these (hence "united atom"), and IIRC there are no .n2t files for any of them. 
So it's not a matter of changing an .n2t file, it's a matter of creating one.


-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] Adding manual LJ interaction value in charmm27?

[Justin Lemkul]

On 1/3/13 3:34 AM, 라지브간디 wrote:

Dear gmx users,


I would like to know to how to set the particular atom, Lennard Jones potential 
function (12-6) value of sigma and epsilon in CHARMM27 force field?


For example, i want to give the manual LJ interaction value for C atom in 
charmm27? should i give my value in ffnonboneded.itp ??? Plz advice me.



Yes.  That's where nonbonded parameters are specified.

-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] trjconv - more than one box

[Justin Lemkul]

On 1/3/13 5:09 AM, Weingarth, M.H. (Markus) wrote:

Dear Gromacs users,

I was wondering if one can use trjconv to get a .pdb file which shows more than 
one box?

Just like the "genconf -nbox" command but with trajectories?



genconf has an option called -trj that sounds like it might do what you want, 
but I've never tried it.  Otherwise, you can script the process you want with 
multiple trjconv and genconf steps:


1. Use trjconv to split frames into separate coordinate files
2. Loop over coordinate files to run genconf -nbox
3. Use trjconv to reassemble a new trajectory from all the frames from step 2

-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] gromacs demo

[Justin Lemkul]

On 1/3/13 6:06 AM, amna khan wrote:

hi all.

i am a beginer user of ubuntu and gromacs
i installed gormacs on ubuntu 12.10 and now want to run demo , i dont know
how to run this correctly

i do by typing cd /usr/share/gromacs/tutor/gmxdemo

it gives nothing as output



You changed into a directory; you didn't actually run anything.  There's a 
script called 'demo' in that directory that you need to execute to get it to run.




help me please in running the demo



The demo is significantly less useful than the many tutorials provided online.

http://www.gromacs.org/Documentation/Tutorials

-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: Fw: [gmx-users] Amidated C-terminal

[Justin Lemkul]

On 1/3/13 6:11 AM, Shima Arasteh wrote:

Have a look at CT2 in aminoacids.c.tdb please:

[ CT2 ]
[ replace ]
  OCC12.0110.55
  OO15.9994-0.55


It is +0.55 as what you said. But I see all carbonyl C in aminoacids.rtp file 
have +0.51 charge.
I think the amidated C-terminal in my top file should be charged +0.55 as what 
I see in c.tdb. Shouldn't be? Why it couldn't understand to take +0.55 charge 
for this last residue?



There is an error in the .tdb file.  The first [replace] line attempts to 
replace an O atom and assign it a CC type with charge of +0.55, which is then 
overridden by the next line, which assigns the O atom an O type with -0.55 
charge.  The carbonyl C is (erroneously) not adjusted.  The correct line is 
present in the charmm27.ff folder:


[ CT2 ]
[ replace ]
 C  CC  12.011  0.55
 O  O   15.9994 -0.55

-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: Fw: [gmx-users] Amidated C-terminal

[Shima Arasteh]

Have a look at CT2 in aminoacids.c.tdb please:

[ CT2 ]
[ replace ]
 O        CC        12.011    0.55
 O        O        15.9994    -0.55


It is +0.55 as what you said. But I see all carbonyl C in aminoacids.rtp file 
have +0.51 charge.
I think the amidated C-terminal in my top file should be charged +0.55 as what 
I see in c.tdb. Shouldn't be? Why it couldn't understand to take +0.55 charge 
for this last residue?

 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Thursday, January 3, 2013 2:24 PM
Subject: Re: Fw: [gmx-users] Amidated C-terminal



On 1/3/13 1:00 AM, Shima Arasteh wrote:
>
>
>
>
>
>
> The version of GROMACS I'm using is 4.5.5.
> I checked the aminiacids.rtp file in charmm36 folder, I see + 0.51 for 
> carbonyl C. Is there any problem with the C36 which I use?
>

Probably.  Check the aminoacids.c.tdb file as well, it may not be correct.  I 
used the standard charmm27.ff for my test and it worked fine.

-Justin

> [ SER ]
>   [ atoms ]
>      N    NH1    -0.47    0
>      HN    H    0.31    1
>      CA    CT1    0.07    2
>      HA    HB    0.09    3
>      CB    CT2    0.05    4
>      HB1    HA    0.09    5
>      HB2    HA    0.09    6
>      OG    OH1    -0.66    7
>      HG1    H    0.43    8
>      C    C    0.51    9
>      O    O    -0.51    10
>
>
>
>
> Sincerely,
> Shima
>
>
> 
> From: Justin Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Sent: Wednesday, January 2, 2013 10:46 PM
> Subject: Re: [gmx-users] Amidated C-terminal
>
>
>
> On 1/2/13 2:07 PM, Shima Arasteh wrote:
>>
>>
>>     Hi,
>>
>> In order to make an amidated c-terminal, I used CT2 in charmm ff at the 
>> c-terminal. The last residue of my peptide is serine, and the total charge 
>> of peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at 
>> the c-terminal, and then getting top file, when I see the top file, 
>> everything is ok up to the amidated serine residue. But something wrong is 
>> with the charged amidated serine; the total charge is not equal to 5.00 :
>>
>>       .
>>       .
>>       .
>>       361          C     22    LYS      C    361       0.51     12.011   ; 
>>qtot 5.51
>>       362          O     22    LYS      O    362      -0.51     15.999   ; 
>>qtot 5
>> ; residue  23 SER rtp SER  q -0.0
>>       363        NH1     23    SER      N    363      -0.47     14.007   ; 
>>qtot 4.53
>>       364          H     23    SER     HN    364       0.31      1.008   ; 
>>qtot 4.84
>>       365        CT1     23    SER     CA    365       0.07     12.011   ; 
>>qtot 4.91
>>       366         HB     23    SER     HA    366       0.09      1.008   ; 
>>qtot 5
>>       367        CT2     23    SER     CB    367       0.05     12.011   ; 
>>qtot 5.05
>>       368         HA     23    SER    HB1    368       0.09      1.008   ; 
>>qtot 5.14
>>       369         HA     23    SER    HB2    369       0.09      1.008   ; 
>>qtot 5.23
>>       370        OH1     23    SER     OG    370      -0.66     15.999   ; 
>>qtot 4.57
>>       371          H     23    SER    HG1    371       0.43      1.008   ; 
>>qtot 5
>>       372          C     23    SER      C    372       0.51     12.011   ; 
>>qtot 5.51
>>       373        NH2     23    SER     NT    373      -0.62     14.007   ; 
>>qtot 4.89
>>       374          H     23    SER    HT1    374        0.3      1.008   ; 
>>qtot 5.19
>>       375          H     23    SER    HT2    375       0.32      1.008   ; 
>>qtot 5.51
>>       376          O     23    SER      O    376      -0.55     15.999   ; 
>>qtot 4.96
>>
>> I'm wondering if it is incorrect to use CT2 as the c-terminal? Why the last 
>> residue is positive charged? Do the defined atom charges are supposed to be 
>> modified in last residue ?
>>
>
> The choice of CT2 is correct.  The net charge comes from an incorrect charge
> assignment to the carbonyl C (atom 372), which should be +0.55 instead of 
> +0.51,
> which is the charge in a normal backbone peptide bond.  The aminoacids.c.tdb
> file correctly assigns this charge, so I don't know why pdb2gmx didn't produce
> it.  I tried a protein in version 4.5.5 and it worked perfectly - which 
> version
> are you using?  If it's not 4.5.5, upgrade and try again.
>
> -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: Fw: [gmx-users] Amidated C-terminal

[Justin Lemkul]

On 1/3/13 1:00 AM, Shima Arasteh wrote:







The version of GROMACS I'm using is 4.5.5.
I checked the aminiacids.rtp file in charmm36 folder, I see + 0.51 for carbonyl 
C. Is there any problem with the C36 which I use?



Probably.  Check the aminoacids.c.tdb file as well, it may not be correct.  I 
used the standard charmm27.ff for my test and it worked fine.


-Justin


[ SER ]
  [ atoms ]
 NNH1-0.470
 HNH0.311
 CACT10.072
 HAHB0.093
 CBCT20.054
 HB1HA0.095
 HB2HA0.096
 OGOH1-0.667
 HG1H0.438
 CC0.519
 OO-0.5110




Sincerely,
Shima



From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS users 

Sent: Wednesday, January 2, 2013 10:46 PM
Subject: Re: [gmx-users] Amidated C-terminal



On 1/2/13 2:07 PM, Shima Arasteh wrote:



Hi,

In order to make an amidated c-terminal, I used CT2 in charmm ff at the 
c-terminal. The last residue of my peptide is serine, and the total charge of 
peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at the 
c-terminal, and then getting top file, when I see the top file, everything is 
ok up to the amidated serine residue. But something wrong is with the charged 
amidated serine; the total charge is not equal to 5.00 :

  .
  .
  .
  361  C 22LYS  C361   0.51 12.011   ; qtot 
5.51
  362  O 22LYS  O362  -0.51 15.999   ; qtot 
5
; residue  23 SER rtp SER  q -0.0
  363NH1 23SER  N363  -0.47 14.007   ; qtot 
4.53
  364  H 23SER HN364   0.31  1.008   ; qtot 
4.84
  365CT1 23SER CA365   0.07 12.011   ; qtot 
4.91
  366 HB 23SER HA366   0.09  1.008   ; qtot 
5
  367CT2 23SER CB367   0.05 12.011   ; qtot 
5.05
  368 HA 23SERHB1368   0.09  1.008   ; qtot 
5.14
  369 HA 23SERHB2369   0.09  1.008   ; qtot 
5.23
  370OH1 23SER OG370  -0.66 15.999   ; qtot 
4.57
  371  H 23SERHG1371   0.43  1.008   ; qtot 
5
  372  C 23SER  C372   0.51 12.011   ; qtot 
5.51
  373NH2 23SER NT373  -0.62 14.007   ; qtot 
4.89
  374  H 23SERHT13740.3  1.008   ; qtot 
5.19
  375  H 23SERHT2375   0.32  1.008   ; qtot 
5.51
  376  O 23SER  O376  -0.55 15.999   ; qtot 
4.96

I'm wondering if it is incorrect to use CT2 as the c-terminal? Why the last 
residue is positive charged? Do the defined atom charges are supposed to be 
modified in last residue ?



The choice of CT2 is correct.  The net charge comes from an incorrect charge
assignment to the carbonyl C (atom 372), which should be +0.55 instead of +0.51,
which is the charge in a normal backbone peptide bond.  The aminoacids.c.tdb
file correctly assigns this charge, so I don't know why pdb2gmx didn't produce
it.  I tried a protein in version 4.5.5 and it worked perfectly - which version
are you using?  If it's not 4.5.5, upgrade and try again.

-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] fftw3f errors despite having the right libraries in the right places installation on MAC

[maria goranovic]

Did start from scratch, and things were normal this time. thank you !

On Fri, Dec 28, 2012 at 2:22 PM, maria goranovic
wrote:

> thank you, Mark. I will try to restart from scratch
>
>
> On Fri, Dec 28, 2012 at 1:10 AM, Mark Abraham wrote:
>
>> Standard procedure is to do
>>
>> ./configure
>> make
>> sudo make install
>>
>> or
>>
>> ./configure --prefix=/somewhere/you/can/write/to
>> make
>> make install
>>
>> I suggest you use sudo to get rid of your progress to date and start
>> again.
>> Using sudo anywhere else is a recipe for trouble.
>>
>> Mark
>>
>> On Thu, Dec 27, 2012 at 3:41 PM, maria goranovic
>> wrote:
>>
>> > I will try to fix this. Thank you.
>> >
>> > Now, the problem I have is that the executables all belong to root, and
>> as
>> > a user, I am unable to execute them. How to fix this little one?
>> >
>> > Maria
>> >
>> > On Thu, Dec 27, 2012 at 3:36 PM, Mark Abraham > > >wrote:
>> >
>> > > sudo should not be necessary for looking in those directories. Whoever
>> > set
>> > > them up has not set up the permissions on them properly. Fix the
>> problem,
>> > > not the symptoms - you do not want to have to configure software as
>> root,
>> > > or you are trusting every author of that software not to trash your
>> > system
>> > > accidentally.
>> > >
>> > > On Thu, Dec 27, 2012 at 3:31 PM, maria goranovic
>> > > wrote:
>> > >
>> > > > turned out to be a sudo problem. without sudo, the compiler could
>> not
>> > > look
>> > > > into the root directories. sorry for spamming :(
>> > > >
>> > > > On Thu, Dec 27, 2012 at 2:25 PM, maria goranovic
>> > > > wrote:
>> > > >
>> > > > > Yes, I can see them in printenv
>> > > > >
>> > > > > does this have anything to do with single or double precision?
>> > > > >
>> > > > >
>> > > > > On Thu, Dec 27, 2012 at 1:38 PM, Mark Abraham <
>> > > mark.j.abra...@gmail.com
>> > > > >wrote:
>> > > > >
>> > > > >> Are those variables actully showing up in your environment?
>> > > > >>
>> > > > >> On Thu, Dec 27, 2012 at 11:31 AM, maria goranovic
>> > > > >> wrote:
>> > > > >>
>> > > > >> > Dear All
>> > > > >> >
>> > > > >> > I am trying to install 4.5.5 on my mac. I have installed fftw3
>> > with
>> > > > >> > --enable-float, and have used the CPPFLAGS and LDFLAGS options
>> in
>> > my
>> > > > >> > .bashrc file. GROMACS still complains that "configure: error:
>> > Cannot
>> > > > >> find
>> > > > >> > fftw3f library".
>> > > > >> >
>> > > > >> > Why is it not able to find the libraries?
>> > > > >> >
>> > > > >> > Here are the specific details:
>> > > > >> >
>> > > > >> > content of .bashrc:
>> > > > >> >
>> > > > >> > export CPPFLAGS="-I/usr/local/include"
>> > > > >> > export LDFLAGS="-L/usr/local/lib"
>> > > > >> >
>> > > > >> > % ls /usr/local/lib/*fft*
>> > > > >> > /usr/local/lib/libfftw3f.a /usr/local/lib/libfftw3f.la
>> > > > >> >
>> > > > >> > % ls /usr/local/include/*fft*
>> > > > >> > /usr/local/include/fftw3.f /usr/local/include/fftw3.f03
>> > > > >> > /usr/local/include/fftw3.h /usr/local/include/fftw3l.f03
>> > > > >> > /usr/local/include/fftw3q.f03
>> > > > >> >
>> > > > >> > Any ideas what might be going wrong?
>> > > > >> >
>> > > > >> > Thank you
>> > > > >> >
>> > > > >> >
>> > > > >> > --
>> > > > >> > Maria G.
>> > > > >> > Technical University of Denmark
>> > > > >> > Copenhagen
>> > > > >> > --
>> > > > >> > 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
>> > > > >> >
>> > > > >> --
>> > > > >> 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
>> > > > >>
>> > > > >
>> > > > >
>> > > > >
>> > > > > --
>> > > > > Maria G.
>> > > > > Technical University of Denmark
>> > > > > Copenhagen
>> > > > >
>> > > >
>> > > >
>> > > >
>> > > > --
>> > > > Maria G.
>> > > > Technical University of Denmark
>> > > > Copenhagen
>> > > > --
>> > > > 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? Rea

[gmx-users] Re: g_saltbr not include side chains of GLU and ASP??

[Kavyashree M]

Dear users,

I would like to add that in case of ARG or LYS, the sidechain
nitrogen atoms (NE,NZ,NH1,NH2) are present in the output.
The problem s only with GLU and ASP residues.
I use 4.5.3 version

Thank you
kavya

On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M  wrote:

> Dear users,
>
> I used g_saltbr to calculate the salt-bridge interactions using:
> g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep
> It gave the output for each atom-atom interaction within
> the given cut-off.
> When I checked the atom type that corresponds to the atom
> number output in each file, side chain oxygen atoms of ASP
> and GLU was not present in any of  the file. And most of the
> atoms that corresponds to the ASP and GLU were CB, CG or
> CD.
> Kindly someone clarify why is this so.
>
> Thank you
> Kavya
>
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[gmx-users] trjconv - more than one box

[Weingarth, M.H. (Markus)]

Dear Gromacs users,

I was wondering if one can use trjconv to get a .pdb file which shows more than 
one box?

Just like the "genconf -nbox" command but with trajectories?

Thanks a lot
Markus
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[gmx-users] g_saltbr not include side chains of GLU and ASP??

[Kavyashree M]

Dear users,

I used g_saltbr to calculate the salt-bridge interactions using:
g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep
It gave the output for each atom-atom interaction within
the given cut-off.
When I checked the atom type that corresponds to the atom
number output in each file, side chain oxygen atoms of ASP
and GLU was not present in any of  the file. And most of the
atoms that corresponds to the ASP and GLU were CB, CG or
CD.
Kindly someone clarify why is this so.

Thank you
Kavya
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[gmx-users] Adding manual LJ interaction value in charmm27?

[라지브간디]

Dear gmx users,


I would like to know to how to set the particular atom, Lennard Jones potential 
function (12-6) value of sigma and epsilon in CHARMM27 force field? 


For example, i want to give the manual LJ interaction value for C atom in 
charmm27? should i give my value in ffnonboneded.itp ??? Plz advice me.
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