[gmx-users] CHarmm and popc membrane

[Pär Bjelkmar]

Hi,

> I still don't see it (see below), is this [no]chargegrp new in the cvs ? 
> I'm pretty sure that you're not referring to [no]lys, etc.


Yes, that seems to be the case indeed. I've got it in my 'cvs' installation but 
not in my 4.0.7. 

/Pär--
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[gmx-users] dynamic cross correlation map (DCCM)

[leila karami]

Hi

I want to obtain dynamic cross correlation map (DCCM). I used following
command for obtaining covariance matrix.

g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l
covar.log -xpm covar.xpm.

my system consists protein of 70 aminoacids. I want survey correlated and
anti-correlated motion between residues.

Is my manner true? If so, which of output files in above give me dynamic
cross correlation map (DCCM)? otherwise, please guide me.
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Re: [gmx-users] Is there anyone who has tip3p.gro?

[Yang Ye]

You may find it in gromacs source.

On Tue, Jan 19, 2010 at 2:08 PM, xiao shijun  wrote:

> Hi there,
> Recently, I cannot add tip3p water in my system, because GMX
> cannot find tip3p.gro in GMXLIB. I am wondering is there anyone who has
> tip3p.gro, and could you please give me one copy.
> highly appreciate!!
>
> shijun
>
> --
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Regards,
Yang Ye
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[gmx-users] Is there anyone who has tip3p.gro?

[xiao shijun]

Hi there,
Recently, I cannot add tip3p water in my system, because GMX
cannot find tip3p.gro in GMXLIB. I am wondering is there anyone who has
tip3p.gro, and could you please give me one copy.
highly appreciate!!

shijun
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Re: [gmx-users] OPLS AA simulation of beta-lactam system

[Justin A. Lemkul]

Jacob Spooner wrote:



"Justin A. Lemkul"  1/18/2010 3:23 PM >>>



Jacob Spooner wrote:

Hello,

I am planning to run some free energy of solvation calculations on a 
drug/enzyme system.  I want to start out with pen-G as my drug.  I have

found that OPLS atoms 685-687 describe the beta-lactam portion of my drug,
but I see that they are left out of the gromacs ffopls**.itp/atp files.  Is
this because there is a problem with implementing these parameters within
GROMACS ?  Any help on this topic would be greatly appreciated.



In principle, no.  If you have parameters for a certain species you can 
certainly implement them.  You've even identified the files that would need

to be modified to accommodate your new atom types :)

-Justin

Thanks Justin!

Maybe implemented wasn't the best choice of word, because I am aware that I
am able implement parameters that I have produced which are not included in
my chosen force field.  I was more wondering if there is a reason why the
opls list included in GROMACS skips these numbers.


I think this is something that has been reported before - some small subset of 
atom types are not present in the force field parameter files.  You could always 
submit a bugzilla with the fixed files, requesting that they be implemented in 
the future.  Probably just a consequence of continued force field development, 
something gets left out over time.


-Justin




Thanks Jake Spooner





--


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


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Re: [gmx-users] OPLS AA simulation of beta-lactam system

[Jacob Spooner]

>>> "Justin A. Lemkul"  1/18/2010 3:23 PM >>>


Jacob Spooner wrote:
> Hello,
> 
> I am planning to run some free energy of solvation calculations on a
> drug/enzyme system.  I want to start out with pen-G as my drug.  I have found
> that OPLS atoms 685-687 describe the beta-lactam portion of my drug, but I
> see that they are left out of the gromacs ffopls**.itp/atp files.  Is this
> because there is a problem with implementing these parameters within GROMACS
> ?  Any help on this topic would be greatly appreciated.
> 

In principle, no.  If you have parameters for a certain species you can 
certainly implement them.  You've even identified the files that would need to 
be modified to accommodate your new atom types :)

-Justin

Thanks Justin!

Maybe implemented wasn't the best choice of word, because I am aware that I am 
able implement parameters that I have produced which are not included in my 
chosen force field.  I was more wondering if there is a reason why the opls 
list included in GROMACS skips these numbers. 

> Thanks Jake Spooner
> 

-- 


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


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Re: [gmx-users] OPLS AA simulation of beta-lactam system

[Justin A. Lemkul]

Jacob Spooner wrote:

Hello,

I am planning to run some free energy of solvation calculations on a
drug/enzyme system.  I want to start out with pen-G as my drug.  I have found
that OPLS atoms 685-687 describe the beta-lactam portion of my drug, but I
see that they are left out of the gromacs ffopls**.itp/atp files.  Is this
because there is a problem with implementing these parameters within GROMACS
?  Any help on this topic would be greatly appreciated.



In principle, no.  If you have parameters for a certain species you can 
certainly implement them.  You've even identified the files that would need to 
be modified to accommodate your new atom types :)


-Justin


Thanks Jake Spooner



--


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


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[gmx-users] OPLS AA simulation of beta-lactam system

[Jacob Spooner]

Hello,

I am planning to run some free energy of solvation calculations on a 
drug/enzyme system.  I want to start out with pen-G as my drug.  I have found 
that OPLS atoms 685-687 describe the beta-lactam portion of my drug, but I see 
that they are left out of the gromacs ffopls**.itp/atp files.  Is this because 
there is a problem with implementing these parameters within GROMACS ?  Any 
help on this topic would be greatly appreciated.

Thanks
Jake Spooner

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Re: [gmx-users] gromacs 3.3.4

[David van der Spoel]

Julien Michel wrote:

Hi,

I'd like to download gromacs-3-3.4 to replicate results generated with 
this version of the code. I believe this version used to be available on 
the old CVS repository. Could someone please point out instructions to 
download this older version of the code from Git or another source?


Best regards,

Julien


There never was a 3.3.4 release.
The closest you can get is the git branch with release-3-3-patches.
So after git clone you would do
git checkout --track -b release-3-3-patches origin/release-3-3-patches

[kahlo:~/GG/gromacs] % git branch -a
* master
  remotes/origin/2dpme
  remotes/origin/HEAD -> origin/master
  remotes/origin/cpp-analysis
  remotes/origin/generalizedborn
  remotes/origin/history
  remotes/origin/localpressure-4-0
  remotes/origin/master
  remotes/origin/openmm
  remotes/origin/parallelization
  remotes/origin/qhop
  remotes/origin/qmmm
  remotes/origin/release-1-6-02
  remotes/origin/release-3-0-patches
  remotes/origin/release-3-1-patches
  remotes/origin/release-3-2-patches
  remotes/origin/release-3-3-patches


--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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Re: [gmx-users] gromacs 3.3.4

[Justin A. Lemkul]

Julien Michel wrote:

Hi,

I'd like to download gromacs-3-3.4 to replicate results generated with 
this version of the code. I believe this version used to be available on 
the old CVS repository. Could someone please point out instructions to 
download this older version of the code from Git or another source?




You can access all released versions on the ftp site:

ftp://ftp.gromacs.org/pub/gromacs/

-Justin


Best regards,

Julien



--


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


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[gmx-users] gromacs 3.3.4

[Julien Michel]

Hi,

I'd like to download gromacs-3-3.4 to replicate results generated with  
this version of the code. I believe this version used to be available  
on the old CVS repository. Could someone please point out instructions  
to download this older version of the code from Git or another source?


Best regards,

Julien

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Scotland, with registration number SC005336.


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[gmx-users] RE: trjconv problem

[Stefan Hoorman]

>
>
> Hi,
>
> It is not a pdb2gmx feature, but a global one.
> pdb2gmx is only affected in the sense that it retains the residue numbers
> from the input pdb.
> I assume those will be different for most lipid pdb files (if you use
> pdb2gmx for those).
> This renumbering is done by any program that needs to output or select
> global residue numbers.
> Currently this is switchable with the env.var. I mentioned.
> If you put this env.var. in your GMXRC, you can get things how you want
> them.
> Adding an option to all programs is not a good idea.
>
> But I am open for any suggestions on this issue.
>
> There is something I don't get though.
> In the problematic output the lipids can not be one single residue, but
> should be two or more residues.
>
> Berk
>
> > Date: Mon, 18 Jan 2010 10:31:19 -0500
> > From: jalem...@vt.edu
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] trjconv problem
> >
> >
> > Could renumbering be a switchable feature?  For instance, pdb2gmx
> -[no]renumber,
> > with "no" being default?  Otherwise, could you provide an example of how
> to
> > properly use the environment variable you posted, since this would seem
> to
> > affect all of us in the membrane protein world quite distinctly (i.e., a
> > singly-numbered lipid, as reported, kills many of the programs we have
> written
> > for lipid analysis).
> >
> > -Justin
> >
> > Berk Hess wrote:
> > > Hi,
> > >
> > > This is a feature.
> > > For a long time users have been complaining that pdb2gmx renumbers the
> > > residues in a protein.
> > > I have now changed this such that the residue numbers in the pdb are
> > > retained.
> > > But for for instance solvent you would not like to have this behavior.
> > > So I decided to keep numbering single-residue molecules.
> > > If you also want you lipids to continue numbering, you'll have to set
> > > the env.var. GMX_MAXRESRENUM
> > > to the number of residues in a lipid.
> > >
> > > Berk
> > >
> > >
> 
> > > Date: Mon, 18 Jan 2010 13:05:42 -0200
> > > From: stefh...@gmail.com
> > > To: gmx-users@gromacs.org
> > > Subject: [gmx-users] trjconv problem
> > >
> > > I am trying to use trjconv to extract frames from my protein/membrane
> > > system in order to analyse with gdmat. Before using git's latest
> gromacs
> > > version, everything worked just fine. But now, every coordinate file
> > > trjconv gives me has the DPPC lipid molecules without numbering. It is
> > > like if my membrane was formed of a single DPPC (huge) residue. So
> > > instead of generating DPPC residue 1, 2, 3, 4 etc, trjconv gives me
> > > DPPC residue 1 with 5000 atoms.
> > > Some light on the matter would be great.
> > > Thanks
> > >
>

I thank you all for the contributions, but the problem is that the command
"trjconv" is making funny things and not pdb2gmx. My residues are all
numbered correctly. Even my coordinate.gro file that is generated at the end
of the simulation has the correct numbering. The problem is specifically
with "trjconv".
The output from trjconv comes out like this:
"...
66ASN   O  671   3.212   3.554   5.248
66ASN  HO  672   3.258   3.625   5.302
 1DPP C33  673   0.623   5.221   1.344
 1DPP C34  674   0.461   5.360   1.434
 1DPP C35  675   0.697   5.438   1.420
 1DPP   N  676   0.604   5.327   1.444
 1DPP C32  677   0.607   5.278   1.583
 1DPP C31  678   0.722   5.193   1.637
 1DPP O32  679   0.860   5.229   1.645
 1DPP   P  680   0.954   5.102   1.677
 1DPP O33  681   0.882   4.986   1.620
 1DPP O34  682   1.094   5.137   1.647
 1DPP O31  683   0.929   5.088   1.836
 1DPP  C3  684   1.003   5.184   1.912
 1DPP  C2  685   0.946   5.209   2.052
 1DPP O21  686   0.988   5.332   2.111
 1DPP C21  687   0.939   5.454   2.087
 1DPP O22  688   0.893   5.479   1.976
 1DPP C22  689   0.952   5.554   2.195
 1DPP C23  690   1.086   5.626   2.185
 1DPP C24  691   1.132  -0.046   2.310
 1DPP C25  692   1.029   0.049   2.372
 1DPP C26  693   1.080   0.108   2.504
 1DPP C27  694   1.100   0.015   2.624
 1DPP C28  695   1.147   0.089   2.750
 1DPP C29  696   1.047   0.189   2.809
 1DPPC210  697   1.127   0.248   2.925
 1DPPC211  698   1.046   0.363   2.985
 1DPPC212  699   1.127   0.411   3.105
 1DPPC213  700   1.093   0.323   3.226
 1DPPC214  701   1.141   0.402   3.348
 1DPPC215  702   1.107   0.339   3.483
 1DPPC216  703   1.135   0.428   3.604
 1DPP  C1  704   0.997   5.089   2.132
 1DPP O11  705   0.921   5.069   2.251
 1DPP C11  706   0.969   4.974   2.332
 1DPP O12  707   1.070   4.914   2.295
 1DPP C12  708   0.886   4.938   2.449
 1DPP C13  709   0.889   4.790   2.488
 1DPP C14  710   0.996   4.756   2.592
 1DPP C15  711   0.985   4.603   2.597
 1DPP C16  712   1.098   4.556   2.689
 1DPP C17  713   1.061   4.414   2.730
 1DPP C18  714   1.174   4.351

[gmx-users] CHarmm and popc membrane

[Chris Neale]

That's why I said if you know what you're doing :)


ok, fair enough.


The name flag is listed as [no]chargegrp


I still don't see it (see below), is this [no]chargegrp new in the cvs ? 
I'm pretty sure that you're not referring to [no]lys, etc.


$ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z 
2>&1; cat z|grep charge

encads Encad all-atom force field, using scaled-down vacuum charges
encadv Encad all-atom force field, using full solvent charges
-[no]ter bool   no  Interactive termini selection, iso charged
-[no]lys bool   no  Interactive Lysine selection, iso charged
-[no]arg bool   no  Interactive Arganine selection, iso charged
-[no]asp bool   no  Interactive Aspartic Acid selection, iso charged
-[no]glu bool   no  Interactive Glutamic Acid selection, iso charged

##

Chris.

-- original message --

Hi Chris,

/ 
/>/ I believe that the latest response had the wrong subject, so I am  
/>/ changing it back.
/>/ 
/>/ Pär, two comments:

/>/ First, does that option really exist?
/>/ 
/>/ $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z  
/>/ 2>&1; cat z|grep nochargegrp|wc -l
/>/ 
/The name flag is listed as [no]chargegrp


/ 
/>/ Second, I am not entirely convinced that one can discount the need for  
/>/ gromacs-style charge groups. When CHARMM includes an atom in the  
/>/ cutoff, it includes the entire charge group, but that doesn't mean the  
/>/ algorithms of CHARMM and gromacs are entirely the same

/That's why I said if you know what you're doing :)

/ 
/>/ I gather that the large charge group listed below is the one that is  
/>/ spurring the message:
/>/ 
/>/ GROUP  ! H31

/>/ ATOM NNTL-0.60 ! |
/>/ ATOM C11  CTL2   -0.10 ! H33-C13-H32
/>/ ATOM C12  CTL5   -0.35 ! |
/>/ ATOM C13  CTL5   -0.35 !   H21   |   H43
/>/ ATOM C14  CTL5   -0.35 !||   |
/>/ ATOM H11  HL  0.25 !   H22-C12---N---C14-H42   (+)
/>/ ATOM H12  HL  0.25 !||   |
/>/ ATOM H21  HL  0.25 !H23  |   H41
/>/ ATOM H22  HL  0.25 ! |
/>/ ATOM H23  HL  0.25 ! |
/>/ ATOM H31  HL  0.25 ! |
/>/ ATOM H32  HL  0.25 ! H11-C11-H12
/>/ ATOM H33  HL  0.25 ! |
/>/ ATOM H41  HL  0.25 ! |
/>/ ATOM H42  HL  0.25 ! |
/>/ ATOM H43  HL  0.25 ! |
/Yes, and probably one charge group in the arginine residue(s).

/Pär


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RE: [gmx-users] CHarmm and popc membrane (response to "Missing Residues are list ind pdb file")

[Pär Bjelkmar]

Hi Chris,

> 
> I believe that the latest response had the wrong subject, so I am  
> changing it back.
> 
> Pär, two comments:
> First, does that option really exist?
> 
> $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z  
> 2>&1; cat z|grep nochargegrp|wc -l
> 
The name flag is listed as [no]chargegrp

> 
> Second, I am not entirely convinced that one can discount the need for  
> gromacs-style charge groups. When CHARMM includes an atom in the  
> cutoff, it includes the entire charge group, but that doesn't mean the  
> algorithms of CHARMM and gromacs are entirely the same
That's why I said if you know what you're doing :)

> 
> I gather that the large charge group listed below is the one that is  
> spurring the message:
> 
> GROUP  ! H31
> ATOM NNTL-0.60 ! |
> ATOM C11  CTL2   -0.10 ! H33-C13-H32
> ATOM C12  CTL5   -0.35 ! |
> ATOM C13  CTL5   -0.35 !   H21   |   H43
> ATOM C14  CTL5   -0.35 !||   |
> ATOM H11  HL  0.25 !   H22-C12---N---C14-H42   (+)
> ATOM H12  HL  0.25 !||   |
> ATOM H21  HL  0.25 !H23  |   H41
> ATOM H22  HL  0.25 ! |
> ATOM H23  HL  0.25 ! |
> ATOM H31  HL  0.25 ! |
> ATOM H32  HL  0.25 ! H11-C11-H12
> ATOM H33  HL  0.25 ! |
> ATOM H41  HL  0.25 ! |
> ATOM H42  HL  0.25 ! |
> ATOM H43  HL  0.25 ! |
Yes, and probably one charge group in the arginine residue(s).

/Pär-- 
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[gmx-users] CHarmm and popc membrane (response to "Missing Residues are list ind pdb file")

[chris . neale]

Hi Stefan and Pär,

I believe that the latest response had the wrong subject, so I am  
changing it back.


Pär, two comments:
First, does that option really exist?

$ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z  
2>&1; cat z|grep nochargegrp|wc -l



Second, I am not entirely convinced that one can discount the need for  
gromacs-style charge groups. When CHARMM includes an atom in the  
cutoff, it includes the entire charge group, but that doesn't mean the  
algorithms of CHARMM and gromacs are entirely the same, especially  
with respect to:


"Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts."

I admit that it has been 3 years since I used CHARMM, but as I recall  
the requirement for pair interactions to count within the cutoff is  
only that one atom within the charge group is close enough, whereas  
the gromacs warning indicates that in gromacs the interaction is only  
counted when the center of mass of the charge groups are also within  
the cutoff.


Any charmmers out there that can clear this up? I did some searching  
on their archives but I was blocked after 3 searches unless I logged  
in (ugh!).


I gather that the large charge group listed below is the one that is  
spurring the message:


GROUP  ! H31
ATOM NNTL-0.60 ! |
ATOM C11  CTL2   -0.10 ! H33-C13-H32
ATOM C12  CTL5   -0.35 ! |
ATOM C13  CTL5   -0.35 !   H21   |   H43
ATOM C14  CTL5   -0.35 !||   |
ATOM H11  HL  0.25 !   H22-C12---N---C14-H42   (+)
ATOM H12  HL  0.25 !||   |
ATOM H21  HL  0.25 !H23  |   H41
ATOM H22  HL  0.25 ! |
ATOM H23  HL  0.25 ! |
ATOM H31  HL  0.25 ! |
ATOM H32  HL  0.25 ! H11-C11-H12
ATOM H33  HL  0.25 ! |
ATOM H41  HL  0.25 ! |
ATOM H42  HL  0.25 ! |
ATOM H43  HL  0.25 ! |



-- original message --

Hi,

Note, that this is indeed the size of the charge groups in the CHARMM  
force field. You could run pdb2gmx -nochargegrp if you know what  
you're doing.


Regards,
Pär Bjelkmar

I think the notes from grompp are pretty clear. You need to redivide  
 your charge groups so that they contain fewer atoms. You can do  
this  in the .top or .itp file and you can find out how to do that  
in the  manual. Feel free to post your original and  
charge-group-modified  topologies back here if you want people to  
take a look at them.


Chris.

-- original message --

I am trying to equilibrate a POPC membrane with 128 POPC molecules, but
grompp gives out the following notes and minimization with mdrun does not
work. The output on screen of mdrun comes out like this:
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy  =  1.4422483e+17
Maximum force =inf on atom 4082
Norm of force =inf

And grompp notes are:
NOTE 2 [file topol.top, line unknown]:
  The largest charge group contains 12 atoms.



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RE: [gmx-users] trjconv problem

[Berk Hess]

Hi,

It is not a pdb2gmx feature, but a global one.
pdb2gmx is only affected in the sense that it retains the residue numbers from 
the input pdb.
I assume those will be different for most lipid pdb files (if you use pdb2gmx 
for those).
This renumbering is done by any program that needs to output or select global 
residue numbers.
Currently this is switchable with the env.var. I mentioned.
If you put this env.var. in your GMXRC, you can get things how you want them.
Adding an option to all programs is not a good idea.

But I am open for any suggestions on this issue.

There is something I don't get though.
In the problematic output the lipids can not be one single residue, but should 
be two or more residues.

Berk

> Date: Mon, 18 Jan 2010 10:31:19 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] trjconv problem
> 
> 
> Could renumbering be a switchable feature?  For instance, pdb2gmx 
> -[no]renumber, 
> with "no" being default?  Otherwise, could you provide an example of how to 
> properly use the environment variable you posted, since this would seem to 
> affect all of us in the membrane protein world quite distinctly (i.e., a 
> singly-numbered lipid, as reported, kills many of the programs we have 
> written 
> for lipid analysis).
> 
> -Justin
> 
> Berk Hess wrote:
> > Hi,
> > 
> > This is a feature.
> > For a long time users have been complaining that pdb2gmx renumbers the 
> > residues in a protein.
> > I have now changed this such that the residue numbers in the pdb are 
> > retained.
> > But for for instance solvent you would not like to have this behavior.
> > So I decided to keep numbering single-residue molecules.
> > If you also want you lipids to continue numbering, you'll have to set 
> > the env.var. GMX_MAXRESRENUM
> > to the number of residues in a lipid.
> > 
> > Berk
> > 
> > 
> > Date: Mon, 18 Jan 2010 13:05:42 -0200
> > From: stefh...@gmail.com
> > To: gmx-users@gromacs.org
> > Subject: [gmx-users] trjconv problem
> > 
> > I am trying to use trjconv to extract frames from my protein/membrane 
> > system in order to analyse with gdmat. Before using git's latest gromacs 
> > version, everything worked just fine. But now, every coordinate file 
> > trjconv gives me has the DPPC lipid molecules without numbering. It is 
> > like if my membrane was formed of a single DPPC (huge) residue. So 
> > instead of generating DPPC residue 1, 2, 3, 4 etc, trjconv gives me 
> > DPPC residue 1 with 5000 atoms.
> > Some light on the matter would be great.
> > Thanks
> > 
> > 
> > 
> > New Windows 7: Find the right PC for you. Learn more. 
> > 
> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
  
_
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Re: [gmx-users] trjconv problem

[Justin A. Lemkul]

Could renumbering be a switchable feature?  For instance, pdb2gmx -[no]renumber, 
with "no" being default?  Otherwise, could you provide an example of how to 
properly use the environment variable you posted, since this would seem to 
affect all of us in the membrane protein world quite distinctly (i.e., a 
singly-numbered lipid, as reported, kills many of the programs we have written 
for lipid analysis).


-Justin

Berk Hess wrote:

Hi,

This is a feature.
For a long time users have been complaining that pdb2gmx renumbers the 
residues in a protein.
I have now changed this such that the residue numbers in the pdb are 
retained.

But for for instance solvent you would not like to have this behavior.
So I decided to keep numbering single-residue molecules.
If you also want you lipids to continue numbering, you'll have to set 
the env.var. GMX_MAXRESRENUM

to the number of residues in a lipid.

Berk


Date: Mon, 18 Jan 2010 13:05:42 -0200
From: stefh...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] trjconv problem

I am trying to use trjconv to extract frames from my protein/membrane 
system in order to analyse with gdmat. Before using git's latest gromacs 
version, everything worked just fine. But now, every coordinate file 
trjconv gives me has the DPPC lipid molecules without numbering. It is 
like if my membrane was formed of a single DPPC (huge) residue. So 
instead of generating DPPC residue 1, 2, 3, 4 etc, trjconv gives me 
DPPC residue 1 with 5000 atoms.

Some light on the matter would be great.
Thanks



New Windows 7: Find the right PC for you. Learn more. 





--


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


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RE: [gmx-users] trjconv problem

[Berk Hess]

Hi,

This is a feature.
For a long time users have been complaining that pdb2gmx renumbers the residues 
in a protein.
I have now changed this such that the residue numbers in the pdb are retained.
But for for instance solvent you would not like to have this behavior.
So I decided to keep numbering single-residue molecules.
If you also want you lipids to continue numbering, you'll have to set the 
env.var. GMX_MAXRESRENUM
to the number of residues in a lipid.

Berk

Date: Mon, 18 Jan 2010 13:05:42 -0200
From: stefh...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] trjconv problem

I am trying to use trjconv to extract frames from my protein/membrane system in 
order to analyse with gdmat. Before using git's latest gromacs version, 
everything worked just fine. But now, every coordinate file trjconv gives me 
has the DPPC lipid molecules without numbering. It is like if my membrane was 
formed of a single DPPC (huge) residue. So instead of generating DPPC residue 
1, 2, 3, 4 etc, trjconv gives me DPPC residue 1 with 5000 atoms.

Some light on the matter would be great.
Thanks

  
_
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[gmx-users] trjconv problem

[Stefan Hoorman]

I am trying to use trjconv to extract frames from my protein/membrane system
in order to analyse with gdmat. Before using git's latest gromacs version,
everything worked just fine. But now, every coordinate file trjconv gives me
has the DPPC lipid molecules without numbering. It is like if my membrane
was formed of a single DPPC (huge) residue. So instead of generating DPPC
residue 1, 2, 3, 4 etc, trjconv gives me DPPC residue 1 with 5000 atoms.
Some light on the matter would be great.
Thanks
-- 
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Re: [gmx-users] Missing Residues are list ind pdb file

[Pär Bjelkmar]

Hi,

Note, that this is indeed the size of the charge groups in the CHARMM force 
field. You could run pdb2gmx -nochargegrp if you know what you're doing. 

Regards,
Pär Bjelkmar

> I think the notes from grompp are pretty clear. You need to redivide  
> your charge groups so that they contain fewer atoms. You can do this  
> in the .top or .itp file and you can find out how to do that in the  
> manual. Feel free to post your original and charge-group-modified  
> topologies back here if you want people to take a look at them.
> 
> Chris.
> 
> -- original message --
> 
> I am trying to equilibrate a POPC membrane with 128 POPC molecules, but
> grompp gives out the following notes and minimization with mdrun does not
> work. The output on screen of mdrun comes out like this:
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  =  1.4422483e+17
> Maximum force =inf on atom 4082
> Norm of force =inf
> 
> And grompp notes are:
> NOTE 2 [file topol.top, line unknown]:
>   The largest charge group contains 12 atoms.
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