Biswaranjan Meher wrote:
Hello Justin.
Nice to hear from you.
I did the conversion of AMBER files to GROMACS type by the amb2gmx.pl
found in the ffAMBER tools.
I used the command:
g_hbond -f input.pdb -s topol.tpr -n index.ndx -num hbnum.xvg -hbn
hbond.ndx -hbm hbmap.xpm -r 0.4
My input was a pdb file generated from the AMBER trajectory (mdcrd).
I checked the .gro file (onverted from AMBER) with gmxcheck, of which
output is here I am pasting. Just have a look.
Checking file notty.gro
Reading frames from gro file 'notty.gro created by rdparm2gmx.pl Fri Jul
11 17:38:48 IST 2008', 30261 atoms.
Reading frame 0 time 0.000
# Atoms 30261
Precision 0.001 (nm)
Last frame 0 time 0.000
Item #frames Timestep (ps)
Step 0
Time 0
Lambda 0
Coords 1
Velocities 0
Forces 0
Box 1
Can you please suggest , what may be the possible error from this ?
Well, from what it shows here, your "input.pdb" file has only one frame, or at
least, only one frame with valid coordinates and box dimensions. I don't know
much about amb2gmx.pl, but I thought it's intent was to create a .top and .gro
from an AMBER-(xleap-)generated prmtop and inpcrd file. Please someone correct
me if I'm wrong.
Just recently, I developed my own shell script to convert an mdcrd to an .xtc
file, since a member of our lab need for some Gromacs analysis tools. Feel free
to download it from my site:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html
The script has *not* been extensively tested, and I do not promise it will work,
but I am happy to try to help if problems arise. If bugs pop up, it will be
good to know to help make the script better :-)
-Justin
BRM
gcq#254: "O My God, They Killed Kenny !" (South Park)
On Sun, Jul 13, 2008 at 12:19 PM, <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
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Today's Topics:
1. error in g_hbond (Biswaranjan Meher)
2. Re: Can GROMACS mutate a residue? (Lee Soin)
3. Re: error in g_hbond (Justin A. Lemkul)
4. PME User (Sang-Min Park)
5. Re: PME User (David van der Spoel)
6. gromacs bond type (prasun kumar)
----------------------------------------------------------------------
Message: 1
Date: Sat, 12 Jul 2008 17:48:04 +0530
From: "Biswaranjan Meher" <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
Subject: [gmx-users] error in g_hbond
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
Content-Type: text/plain; charset="iso-8859-1"
Dear GROMACS users,
I am new to gmx-users.
I am analysing the H-bonding in my trajectory with the tool g_hbond.
The trajectory was generated by the AMBER force fields.
Now I have converted the AMBER prmtop and inpcrd files to GROMACS
.top and
.gro files.
When I performed the g_hbond, I encountered with a fatal error
Your computational box has shrunk too much.
g_hbond can not handle this situation, sorry.
Also I checked the postings in the archive related to this problem,
but I
didnt get the solution completely.
So is it a problem of my AMBER traj./pdb files I am using or it some
thing
else.
Can anyone will help me in this regard to get the solution ?
Thanks in advance for your kind suggestions.
BRM
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Message: 2
Date: Sat, 12 Jul 2008 20:44:45 +0800
From: "Lee Soin" <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Subject: Re: [gmx-users] Can GROMACS mutate a residue?
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID:
<[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
Content-Type: text/plain; charset="iso-8859-1"
Thanks! And I've learned that Pymol can also do the job.
2008/7/12 DEEPESH AGARWAL <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>:
> Hi,
>
> In addition to what Justin has suggested, VMD has a tool to mutate a
> residue- Extensions>Modeling>Mutate residue.
>
> Deepesh
>
>
> On 7/12/08, Justin A. Lemkul <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
> >
> >
> > Lee Soin wrote:
> >> Hi!
> >> Is there a command in GROMACS that can substitute the atoms of
a whole
> >> residue for another? This is quite useful in doing mutation
simulations.
> >> Or if that's not possible, how should I mutate a residue? Thanks!
> >
> > I would use a program like DeepView (Swiss-PDBViewer), or maybe
Modeller.
> >
> > -Justin
> >
> >>
> >> --
> >> Sun Li
> >> Department of Physics
> >> Nanjing University, China
> >>
> >>
> >>
------------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before
> posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Graduate Research Assistant
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > _______________________________________________
> > gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>.
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> >
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
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> Please don't post (un)subscribe requests to the list. Use the
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>
--
Sun Li
Department of Physics
Nanjing University, China
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Message: 3
Date: Sat, 12 Jul 2008 09:11:24 -0400
From: "Justin A. Lemkul" <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Subject: Re: [gmx-users] error in g_hbond
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Biswaranjan Meher wrote:
> Dear GROMACS users,
> I am new to gmx-users.
>
> I am analysing the H-bonding in my trajectory with the tool g_hbond.
> The trajectory was generated by the AMBER force fields.
> Now I have converted the AMBER prmtop and inpcrd files to GROMACS
.top
> and .gro files.
How did you do this conversion?
>
> When I performed the g_hbond, I encountered with a fatal error
What was the command you issued? Were you analyzing the .gro file,
or some
converted mdcrd file?
>
> Your computational box has shrunk too much.
> g_hbond can not handle this situation, sorry.
>
> Also I checked the postings in the archive related to this
problem, but
> I didnt get the solution completely.
> So is it a problem of my AMBER traj./pdb files I am using or it some
> thing else.
> Can anyone will help me in this regard to get the solution ?
Use gmxcheck on whatever files you have tried to analyze to see if
they contain
the appropriate box vectors. I don't know how you did the
conversion of the
files from AMBER --> GROMACS, so that's a possible source of error.
-Justin
>
> Thanks in advance for your kind suggestions.
>
> BRM
>
>
>
------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 4
Date: Sat, 12 Jul 2008 17:40:06 +0200
From: Sang-Min Park <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
Subject: [gmx-users] PME User
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
Content-Type: text/plain; charset="iso-8859-1"
Dear all,
I read in www.gromacs.org/gromacs/revisions/
<http://www.gromacs.org/gromacs/revisions/> in the report of
David van der Spoel
"Added support for a combination of PME and User determined coulomb
potentials. The user has to take care that the combination of
Coulomb and
standard PME makes sense" ( 8 Feb. 2005)
I don't understand what that means.
As I know the Ewald Sum consist of the reciprocal and direct space term
which are derivated for the f(x)=1/r function.
In this sense I don't know what gromacs would do when I would specify
PME-User with a potential that is different from f(x).
1. Can someone explain me what gromacs is doing when one sets
PME-User ?
2. Furthermore I would like to know if the user defined potential
tables are
also used to calculate the long range interactions.
Thank you for your time
------------------------------
Message: 5
Date: Sat, 12 Jul 2008 17:49:22 +0200
From: David van der Spoel <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
Subject: Re: [gmx-users] PME User
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Sang-Min Park wrote:
> Dear all,
>
> I read in www.gromacs.org/gromacs/revisions/
<http://www.gromacs.org/gromacs/revisions/> in the report of
> David van der Spoel
>
> "Added support for a combination of PME and User determined coulomb
> potentials. The user has to take care that the combination of
Coulomb and
> standard PME makes sense" ( 8 Feb. 2005)
>
> I don't understand what that means.
>
> As I know the Ewald Sum consist of the reciprocal and direct
space term
> which are derivated for the f(x)=1/r function.
>
> In this sense I don't know what gromacs would do when I would
specify
> PME-User with a potential that is different from f(x).
>
> 1. Can someone explain me what gromacs is doing when one sets
PME-User ?
Let's say you want to replace the Coulomb potential Fc(r) by your own
Fuser(r). Then you have to subtract the Long Range part of the coulomb
potential Fc(r,LR) from your F(r) in the short range potential to get
the correct sum. Note that this also dependent on the cut-off, so if you
decide to change the cut-off you need a new lookup table for the
short-range.
>
> 2. Furthermore I would like to know if the user defined potential
tables are
> also used to calculate the long range interactions.
>
> Thank you for your time
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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.
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se
------------------------------
Message: 6
Date: Sun, 13 Jul 2008 12:18:41 +0530
From: "prasun kumar" <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Subject: [gmx-users] gromacs bond type
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
Content-Type: text/plain; charset="iso-8859-1"
dear users,
I am trying to get some information about the bond type,angle type and
dihedral angle type.
can any one please tell me what is the bond type of C-F.angle type for
F-C-F,dihedral angle type of F-C-C-O &F-C-C-H.
Or any one can tell me how to define the gromacs type for bonds,angles.I
tried to read the 5th chapter but not getting any thing.
actually i am lookig forward to include TFE in the rtp file for my
simulation of peptide in TFE.
Please help me.
Thanx in advance
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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