Re: [gmx-users] Conversion of nm to Å
OP, I give you 10/10. First time I laugh out loud reading the GMX mailing list. /J On Wed, Aug 21, 2013 at 5:05 AM, Arunima Shilpi writetoas...@gmail.comwrote: Dear Sir I have to query as to how do we convert the paramaters in nm to Å --. For example the RMSD and RMSF calculation gives result in nm. I want to convert it to Å. I request you to kindly guide me with the process Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 -- João Henriques -- 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] Conversion of nm to Å
Dear Sir I have to query as to how do we convert the paramaters in nm to Å --. For example the RMSD and RMSF calculation gives result in nm. I want to convert it to Å. I request you to kindly guide me with the process Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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
RE: [gmx-users] Conversion of nm to Å
First port of call for a question like this should be a search engine http://en.wikipedia.org/wiki/Angstrom Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Arunima Shilpi Sent: Wednesday, 21 August 2013 1:06 PM To: gmx-users@gromacs.org Subject: [gmx-users] Conversion of nm to Å Dear Sir I have to query as to how do we convert the paramaters in nm to Å --. For example the RMSD and RMSF calculation gives result in nm. I want to convert it to Å. I request you to kindly guide me with the process Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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
[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric), and topologies to Amber format
Dear gmx-users, I followed the suggestions by Justin and Daniel to convert the trajectories, but still Amber does not recognize the correct format and complains about the fact that it does not find the correct box dimensions. It seems that the two tools are quite incompatible, especially when the trajectory is not in the classic cubic format. This is just for records since it is a recurrent query in the gmx-user archive, still apparently with no solution. Many thanks in any case and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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
Re: [gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric), and topologies to Amber format
probably you can try catdcd On 01/21/2013 11:29 AM, Anna Marabotti wrote: Dear gmx-users, I followed the suggestions by Justin and Daniel to convert the trajectories, but still Amber does not recognize the correct format and complains about the fact that it does not find the correct box dimensions. It seems that the two tools are quite incompatible, especially when the trajectory is not in the classic cubic format. This is just for records since it is a recurrent query in the gmx-user archive, still apparently with no solution. Many thanks in any case and best regards Anna -- 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] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format
Dear all, we'd need to convert a trajectory in .xtc format (and the related topology file) to a format that could be read by Amber program (I'd need to perform MM-PBSA calculations). We tried to do it using VMD, but failed to produce a correct trajectory to be read by MMPBSA.py tool. It complains about the fact that it expected only 3 or 6 box coords, but I ran the trajectory using a rhombic dodecahedric box, with 9 box coords. I read the gmx-user archive to find hints to overcome the problem, but only found incomplete, and in some cases quite old, suggestions (We are currently using Gromacs 4.5.4 version). I don't see anywhere a detailed suggestion on how to proceed, and I have even the doubt that this is not possible to do. Could you please give me some information about, possibly with detailed descriptions about the commands and the flags to use? Many thanks in advance for your kind answer and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 When a man with a gun meets a man with a pen, the man with the gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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
Re: [gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format
On 1/17/13 6:22 AM, Anna Marabotti wrote: Dear all, we'd need to convert a trajectory in .xtc format (and the related topology file) to a format that could be read by Amber program (I'd need to perform MM-PBSA calculations). We tried to do it using VMD, but failed to produce a correct trajectory to be read by MMPBSA.py tool. It complains about the fact that it expected only 3 or 6 box coords, but I ran the trajectory using a rhombic dodecahedric box, with 9 box coords. I read the gmx-user archive to find hints to overcome the problem, but only found incomplete, and in some cases quite old, suggestions (We are currently using Gromacs 4.5.4 version). I don't see anywhere a detailed suggestion on how to proceed, and I have even the doubt that this is not possible to do. Could you please give me some information about, possibly with detailed descriptions about the commands and the flags to use? You can write a new box using trjconv and make it whatever you want. Presumably you're stripping out water and such anyway, so all you would have to do is center your solute in whatever box you want: trjconv -s topol.tpr -f traj.xtc -center -box x y z -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 -- 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
Re: [gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format
On Jan 17, 2013, at 12:27 , Justin Lemkul wrote: On 1/17/13 6:22 AM, Anna Marabotti wrote: Dear all, we'd need to convert a trajectory in .xtc format (and the related topology file) to a format that could be read by Amber program (I'd need to perform MM-PBSA calculations). We tried to do it using VMD, but failed to produce a correct trajectory to be read by MMPBSA.py tool. It complains about the fact that it expected only 3 or 6 box coords, but I ran the trajectory using a rhombic dodecahedric box, with 9 box coords. I read the gmx-user archive to find hints to overcome the problem, but only found incomplete, and in some cases quite old, suggestions (We are currently using Gromacs 4.5.4 version). I don't see anywhere a detailed suggestion on how to proceed, and I have even the doubt that this is not possible to do. Could you please give me some information about, possibly with detailed descriptions about the commands and the flags to use? The magic bullet for converting rhombic dodecahedron box trajectories into something that makes intuitive sense is to use trjconv with the flags -ur compact and -pbc mol. Then trjconv will pick the periodic copy of each molecule that has its mass center the closest to the box center instead of the default of choosing the periodic image that has the mass center inside of the triclinic box. You can write a new box using trjconv and make it whatever you want. Presumably you're stripping out water and such anyway, so all you would have to do is center your solute in whatever box you want: -Justin I agree with Justin. It is probably best to strip of all water and create a new box if amber cannot understand triclinic boxes. Use the -center or the -fit flag if the solute diffuses out from the original periodic copy of the box. (But be wary to use -fit with operations that rotate the box!) I recommend that you save the original trajectory. Daniel -- 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] conversion of gromacs topology format
Hi gromacs users, Is there a way to convert gromacs topology format to Amber. Thanks, Aiswarya -- 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
Re: [gmx-users] conversion of gromacs topology format
On 8/09/2011 6:06 PM, aiswarya pawar wrote: Hi gromacs users, Is there a way to convert gromacs topology format to Amber. Did you try Googling for such a tool first? :) There probably isn't one, because starting from scratch with leap is sufficiently easy that a conversion tool is not worth the development and maintenance time. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Conversion of gromacs trajectory file
Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. Thank you, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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
Re: [gmx-users] Conversion of gromacs trajectory file
aiswarya.pa...@gmail.com wrote: Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. The key is finding a compatible intermediate that can be converted. I've found that PDB format is pretty universal. I have a script that does the opposite (mdcrd to .xtc) linked from my site: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html It's a bit awkward, but does the job. Perhaps you can reverse-engineer it for your purpose. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] Conversion of gromacs trajectory file
Hi Justin, Thank for the quick response. I would try out your script for the conversion. Best, Aiswarya --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Discussion list for GROMACS users ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Conversion of gromacs trajectory file Sent: 24 Aug 2011 5:35 PM aiswarya.pa...@gmail.com wrote: Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. The key is finding a compatible intermediate that can be converted. I've found that PDB format is pretty universal. I have a script that does the opposite (mdcrd to .xtc) linked from my site: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html It's a bit awkward, but does the job. Perhaps you can reverse-engineer it for your purpose. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 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] Conversion of the GLYCAM dihedral parameters
Thank you Olivier for your response.
SA
--
Message: 2
Date: Thu, 28 Jul 2011 11:20:44 +0100
From: Oliver Grant olivercgr...@gmail.com
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
CAFd05fG5yAzPHr=ssficaa0ff0q7uet3ib_yjrs70qme3n3...@mail.gmail.com
Content-Type: text/plain; charset=windows-1252
Hi SA,
I think this is due to the original amb2gmx.pl coder only considering
AMBER
type dihedrals. He/She didn't expect any negative values. You'll notice
certain groups like NAc and COO- on sugars are affected when you run your
simulation. Below is a similar post with a fix to the amb2gmx.pl code.
It's
short so I pasted it rather than linking.
You may already know this but note also the default is to correctly fudge
AMBERS 1-4 interactions. So if you run a sugar using the GLYCAM forcefield
they will be incorrectly scaled/fudged. An easy fix is to copy the
ffamber99sb.itp (may be called something else now) to your local directory
where you are running the md and change to:
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0
1.0
If you have a sugar and a protein you cannot mix the scaling. Mixed scaling
is possible in amber11 if you really need it. I did all this when 4.0.7 was
the latest release so things may have changed and it may now be possible to
mix scaling or it may be that something else has changed :)
If you find anything when testing the parameters please do post back.
All the best,
Oliver
*Hi all,
There is a problem that I encountered when I was trying to manually
verify the proper dihedral conversion from AMBER topology to GROMACS
topology using amb2gmx perl script.
Some of the dihedrals were set to zero by amb2gmx even if in the
prmtop file they were not zero. This was happening for all the lines
that had PK with negative values!. Reading the script I came up with
the following lines for V[i] calculation (lines 749 to 755 in the
script file):
...
# get all force constants for each line of a dihedral #
my $lines = $i -1 +$numijkl;
for(my $j=$i;$j=$lines;$j++){
my $period = abs($pn{$j});
if($pk{$j}0) {
$V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
}
...
It seems from here that only PK values 0 are considered when
computing the RB constants.
After I change the sign to != (i.e. not equal to) everything
goes fine and ALL the dihedral are transformed correctly.
While this is OK with different AMBER sets and GAFF if one wish to
convert a GLYCAM (which comes also with Amber package) generated
topology, in the gromacs resultant file there will be missing
parameters for dihedrals. That's because GLYCAM does not use phase
shift and have also negative values for several PK
Is this a bug or there is a reason for considering only the positive
values of PK or I am missing something (as I am a begginer with
AMBER)?
(or maybe amb2gmx was designed only to work an AMBER ff conversion and
not for example GLYCAM)
Thanks for any comment,
Andrei*
On 21 July 2011 10:48, sa sagmx.m...@gmail.com wrote:
Yeah I have also found this page. Finally I did the conversion. I am
currently testing the parameters.
Thank you Austin and Mark for your help
SA-
--
Message: 4
Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT)
From: Austin B. Yongye ybau...@yahoo.com
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
in the GROMACS format.
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
1311171438.14853.yahoomailclas...@web161422.mail.bf1.yahoo.com
Content-Type: text/plain; charset=utf-8
So my questions are: how to convert it in the gromacs format ?
I haven't done AMBER to GROMACS conversions. But a google search led me
to
this page. It's just a matter of knowing the different formats.
http://ffamber.cnsm.csulb.edu
Is it correct to use the absolute value of the multiplicity in my
parameters and use the negative values of barrier heights when they are
exist in the AMBER parameters? Since, I have noticed that in the AMBER
ff port in GROMACS, the multiplicity values are always set to 0
and the barrier heights have sometime a negative value.
So my questions are: how to convert it in the gromacs format ? Is it
correct to use the absolute value of the multiplicity in my parameters
and
use the negative values of barrier heights when they are exist in the
AMBER
parameters? Since, I have noticed that in the AMBER ff port in GROMACS,
the
multiplicity values are always set to 0 and the barrier heights have
sometime a negative value.
Thank you again for your advice.
SA-
Message: 1
Date
Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
Hi SA,
I think this is due to the original amb2gmx.pl coder only considering AMBER
type dihedrals. He/She didn't expect any negative values. You'll notice
certain groups like NAc and COO- on sugars are affected when you run your
simulation. Below is a similar post with a fix to the amb2gmx.pl code. It's
short so I pasted it rather than linking.
You may already know this but note also the default is to correctly fudge
AMBERS 1-4 interactions. So if you run a sugar using the GLYCAM forcefield
they will be incorrectly scaled/fudged. An easy fix is to copy the
ffamber99sb.itp (may be called something else now) to your local directory
where you are running the md and change to:
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0
1.0
If you have a sugar and a protein you cannot mix the scaling. Mixed scaling
is possible in amber11 if you really need it. I did all this when 4.0.7 was
the latest release so things may have changed and it may now be possible to
mix scaling or it may be that something else has changed :)
If you find anything when testing the parameters please do post back.
All the best,
Oliver
*Hi all,
There is a problem that I encountered when I was trying to manually
verify the proper dihedral conversion from AMBER topology to GROMACS
topology using amb2gmx perl script.
Some of the dihedrals were set to zero by amb2gmx even if in the
prmtop file they were not zero. This was happening for all the lines
that had PK with negative values!. Reading the script I came up with
the following lines for V[i] calculation (lines 749 to 755 in the
script file):
...
# get all force constants for each line of a dihedral #
my $lines = $i -1 +$numijkl;
for(my $j=$i;$j=$lines;$j++){
my $period = abs($pn{$j});
if($pk{$j}0) {
$V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
}
...
It seems from here that only PK values 0 are considered when
computing the RB constants.
After I change the sign to != (i.e. not equal to) everything
goes fine and ALL the dihedral are transformed correctly.
While this is OK with different AMBER sets and GAFF if one wish to
convert a GLYCAM (which comes also with Amber package) generated
topology, in the gromacs resultant file there will be missing
parameters for dihedrals. That's because GLYCAM does not use phase
shift and have also negative values for several PK
Is this a bug or there is a reason for considering only the positive
values of PK or I am missing something (as I am a begginer with
AMBER)?
(or maybe amb2gmx was designed only to work an AMBER ff conversion and
not for example GLYCAM)
Thanks for any comment,
Andrei*
On 21 July 2011 10:48, sa sagmx.m...@gmail.com wrote:
Yeah I have also found this page. Finally I did the conversion. I am
currently testing the parameters.
Thank you Austin and Mark for your help
SA-
--
Message: 4
Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT)
From: Austin B. Yongye ybau...@yahoo.com
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
in the GROMACS format.
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
1311171438.14853.yahoomailclas...@web161422.mail.bf1.yahoo.com
Content-Type: text/plain; charset=utf-8
So my questions are: how to convert it in the gromacs format ?
I haven't done AMBER to GROMACS conversions. But a google search led me to
this page. It's just a matter of knowing the different formats.
http://ffamber.cnsm.csulb.edu
Is it correct to use the absolute value of the multiplicity in my
parameters and use the negative values of barrier heights when they are
exist in the AMBER parameters? Since, I have noticed that in the AMBER
ff port in GROMACS, the multiplicity values are always set to 0
and the barrier heights have sometime a negative value.
So my questions are: how to convert it in the gromacs format ? Is it
correct to use the absolute value of the multiplicity in my parameters and
use the negative values of barrier heights when they are exist in the AMBER
parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the
multiplicity values are always set to 0 and the barrier heights have
sometime a negative value.
Thank you again for your advice.
SA-
Message: 1
Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT)
From: Austin B. Yongye ybau...@yahoo.com
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
in the GROMACS format.
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
1311098935.93905.yahoomailclas...@web161426.mail.bf1.yahoo.com
Content-Type: text/plain; charset=utf-8
It is normal to have combinations of negative and positive values for the
barrier heights. Those are just the best coefficients to reproduce some QM
rotational energy curve
[gmx-users] Conversion of the GLYCAM dihedral parameters
Yeah I have also found this page. Finally I did the conversion. I am currently testing the parameters. Thank you Austin and Mark for your help SA- -- Message: 4 Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT) From: Austin B. Yongye ybau...@yahoo.com Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1311171438.14853.yahoomailclas...@web161422.mail.bf1.yahoo.com Content-Type: text/plain; charset=utf-8 So my questions are: how to convert it in the gromacs format ? I haven't done AMBER to GROMACS conversions. But a google search led me to this page. It's just a matter of knowing the different formats. http://ffamber.cnsm.csulb.edu Is it correct to use the absolute value of the multiplicity in my parameters and use the negative values of barrier heights when they are exist in the AMBER parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the multiplicity values are always set to 0 and the barrier heights have sometime a negative value. So my questions are: how to convert it in the gromacs format ? Is it correct to use the absolute value of the multiplicity in my parameters and use the negative values of barrier heights when they are exist in the AMBER parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the multiplicity values are always set to 0 and the barrier heights have sometime a negative value. Thank you again for your advice. SA- Message: 1 Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT) From: Austin B. Yongye ybau...@yahoo.com Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1311098935.93905.yahoomailclas...@web161426.mail.bf1.yahoo.com Content-Type: text/plain; charset=utf-8 It is normal to have combinations of negative and positive values for the barrier heights. Those are just the best coefficients to reproduce some QM rotational energy curve during the parameterization. The negative periodicities are a convention from AMBER. They simply indicate that the dihedral angle potential has more than one term. For your example below: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 -3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive value is reached, terms for the O2-P-OS-CP potential have been completely accounted for. Hope that helps. Austin- --- On Tue, 7/19/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, July 19, 2011, 7:08 AM On 19/07/2011 11:56 PM, sa wrote: Dear GROMCS users, I am trying to convert some GLYCAM parameters in GROMACS format. For this purpose, I am using the latest GLYCAM parameters downloaded from the RJ. Woods’ website and the examples given in the acpype code (here for the dihedral angles) : http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 --- # dihedralidivfbarrier hight/2 kcal/mol phase degrees periodicity comments X -ca-ca-X4 14.500* 180.000 2.000 intrpol.bsd.on C6H6 * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in topolbuild, why?) = 30.334 or 15.167 kJ/mol # X -CA-CA-X4 14.50180.0 2. intrpol.bsd.on C6H6 (from parm99.dat) # X-CA-CA-X 330.33400 0.0 -30.33400 0.0 0.0 0.0 ; intrpol.bsd.on C6H6 --- I have no problems with the parameters for proteins. But, in case of the GLYCAM parameters, I am a little confused about the conversion of dihedral force constants (DFC), especially when the DFC and the periodicity values are 0 for example for this torsion: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 Where only a positive value makes sense, sometimes people use negative values to indicate some special functional form. This can be easier to code. Regardless, you'll have to check out the GLYCAM documentation and see what is meant, before you
[gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.
Thank you Austin, for the clarification, So my questions are: how to convert it in the gromacs format ? Is it correct to use the absolute value of the multiplicity in my parameters and use the negative values of barrier heights when they are exist in the AMBER parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the multiplicity values are always set to 0 and the barrier heights have sometime a negative value. Thank you again for your advice. SA- Message: 1 Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT) From: Austin B. Yongye ybau...@yahoo.com Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1311098935.93905.yahoomailclas...@web161426.mail.bf1.yahoo.com Content-Type: text/plain; charset=utf-8 It is normal to have combinations of negative and positive values for the barrier heights. Those are just the best coefficients to reproduce some QM rotational energy curve during the parameterization. The negative periodicities are a convention from AMBER. They simply indicate that the dihedral angle potential has more than one term. For your example below: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 -3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive value is reached, terms for the O2-P-OS-CP potential have been completely accounted for. Hope that helps. Austin- --- On Tue, 7/19/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, July 19, 2011, 7:08 AM On 19/07/2011 11:56 PM, sa wrote: Dear GROMCS users, I am trying to convert some GLYCAM parameters in GROMACS format. For this purpose, I am using the latest GLYCAM parameters downloaded from the RJ. Woods’ website and the examples given in the acpype code (here for the dihedral angles) : http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 --- # dihedralidivfbarrier hight/2 kcal/mol phase degrees periodicity comments X -ca-ca-X4 14.500* 180.000 2.000 intrpol.bsd.on C6H6 * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in topolbuild, why?) = 30.334 or 15.167 kJ/mol # X -CA-CA-X4 14.50180.0 2. intrpol.bsd.on C6H6 (from parm99.dat) # X-CA-CA-X 330.33400 0.0 -30.33400 0.0 0.0 0.0 ; intrpol.bsd.on C6H6 --- I have no problems with the parameters for proteins. But, in case of the GLYCAM parameters, I am a little confused about the conversion of dihedral force constants (DFC), especially when the DFC and the periodicity values are 0 for example for this torsion: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 Where only a positive value makes sense, sometimes people use negative values to indicate some special functional form. This can be easier to code. Regardless, you'll have to check out the GLYCAM documentation and see what is meant, before you can address how to convert it into a GROMACS format. Obviously the contents of parts of chapter 4 and 5 of the manual will be important. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.
So my questions are: how to convert it in the gromacs format ? I haven't done AMBER to GROMACS conversions. But a google search led me to this page. It's just a matter of knowing the different formats. http://ffamber.cnsm.csulb.edu Is it correct to use the absolute value of the multiplicity in my parameters and use the negative values of barrier heights when they are exist in the AMBER parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the multiplicity values are always set to 0 and the barrier heights have sometime a negative value. So my questions are: how to convert it in the gromacs format ? Is it correct to use the absolute value of the multiplicity in my parameters and use the negative values of barrier heights when they are exist in the AMBER parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the multiplicity values are always set to 0 and the barrier heights have sometime a negative value. Thank you again for your advice. SA- Message: 1 Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT) From: Austin B. Yongye ybau...@yahoo.com Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1311098935.93905.yahoomailclas...@web161426.mail.bf1.yahoo.com Content-Type: text/plain; charset=utf-8 It is normal to have combinations of negative and positive values for the barrier heights. Those are just the best coefficients to reproduce some QM rotational energy curve during the parameterization. The negative periodicities are a convention from AMBER. They simply indicate that the dihedral angle potential has more than one term. For your example below: O2-P -OS-CP 1 0.10 0.0 -3. Dimethyl phosphate 1 -0.50 0.0 -2. 1 0.10 0.0 1 -3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive value is reached, terms for the O2-P-OS-CP potential have been completely accounted for. Hope that helps. Austin- --- On Tue, 7/19/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, July 19, 2011, 7:08 AM On 19/07/2011 11:56 PM, sa wrote: Dear GROMCS users, I am trying to convert some GLYCAM parameters in GROMACS format. For this purpose, I am using the latest GLYCAM parameters downloaded from the RJ. Woods’ website and the examples given in the acpype code (here for the dihedral angles) : http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 --- # dihedral idivf barrier hight/2 kcal/mol phase degrees periodicity comments X -ca-ca-X 4 14.500* 180.000 2.000 intrpol.bsd.on C6H6 * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in topolbuild, why?) = 30.334 or 15.167 kJ/mol # X -CA-CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 (from parm99.dat) # X-CA-CA-X 3 30.33400 0.0 -30.33400 0.0 0.0 0.0 ; intrpol.bsd.on C6H6 --- I have no problems with the parameters for proteins. But, in case of the GLYCAM parameters, I am a little confused about the conversion of dihedral force constants (DFC), especially when the DFC and the periodicity values are 0 for example for this torsion: O2-P -OS-CP 1 0.10 0.0 -3. Dimethyl phosphate 1 -0.50 0.0 -2. 1 0.10 0.0 1 Where only a positive value makes sense, sometimes people use negative values to indicate some special functional form. This can be easier to code. Regardless, you'll have to check out the GLYCAM documentation and see what is meant, before you can address how to convert it into a GROMACS format. Obviously the contents of parts of chapter 4 and 5 of the manual will be important. Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org
Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.
On 20/07/2011 7:33 PM, sa wrote: Thank you Austin, for the clarification, So my questions are: how to convert it in the gromacs format ? Is it correct to use the absolute value of the multiplicity in my parameters and use the negative values of barrier heights when they are exist in the AMBER parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the multiplicity values are always set to 0 and the barrier heights have sometime a negative value. You want to implement the same mathematical function in each case. Take the GLYCAM parameters, drop them into the correct function. Then consult chapters 4 and 5 of the GROMACS manual and see what will be necessary to reproduce that function. Then test on a tiny system that you can also compute by hand to confirm your understanding. Mark Thank you again for your advice. SA- Message: 1 Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT) From: Austin B. Yongye ybau...@yahoo.com mailto:ybau...@yahoo.com Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 1311098935.93905.yahoomailclas...@web161426.mail.bf1.yahoo.com mailto:1311098935.93905.yahoomailclas...@web161426.mail.bf1.yahoo.com Content-Type: text/plain; charset=utf-8 It is normal to have combinations of negative and positive values for the barrier heights. Those are just the best coefficients to reproduce some QM rotational energy curve during the parameterization. The negative periodicities are a convention from AMBER. They simply indicate that the dihedral angle potential has more than one term. For your example below: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 -3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive value is reached, terms for the O2-P-OS-CP potential have been completely accounted for. Hope that helps. Austin- --- On Tue, 7/19/11, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Date: Tuesday, July 19, 2011, 7:08 AM On 19/07/2011 11:56 PM, sa wrote: Dear GROMCS users, I am trying to convert some GLYCAM parameters in GROMACS format. For this purpose, I am using the latest GLYCAM parameters downloaded from the RJ. Woods' website and the examples given in the acpype code (here for the dihedral angles) : http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 --- # dihedralidivfbarrier hight/2 kcal/mol phase degrees periodicity comments X -ca-ca-X4 14.500* 180.0002.000 intrpol.bsd.on C6H6 * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in topolbuild, why?) = 30.334 or 15.167 kJ/mol # X -CA-CA-X4 14.50180.0 2. intrpol.bsd.on C6H6 (from parm99.dat) # X-CA-CA-X 330.33400 0.0 -30.33400 0.0 0.0 0.0 ; intrpol.bsd.on C6H6 --- I have no problems with the parameters for proteins. But, in case of the GLYCAM parameters, I am a little confused about the conversion of dihedral force constants (DFC), especially when the DFC and the periodicity values are 0 for example for this torsion: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 Where only a positive value makes sense, sometimes people use negative values to indicate some special functional form. This can be easier to code. Regardless, you'll have to check out the GLYCAM documentation and see what is meant, before you can address how to convert it into a GROMACS format. Obviously the contents of parts of chapter 4 and 5 of the manual will be important. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive
[gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.
Dear GROMCS users, I am trying to convert some GLYCAM parameters in GROMACS format. For this purpose, I am using the latest GLYCAM parameters downloaded from the RJ. Woods’ website and the examples given in the acpype code (here for the dihedral angles) : http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 --- # dihedralidivfbarrier hight/2 kcal/mol phase degrees periodicity comments X -ca-ca-X4 14.500* 180.000 2.000 intrpol.bsd.on C6H6 * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in topolbuild, why?) = 30.334 or 15.167 kJ/mol # X -CA-CA-X4 14.50180.0 2. intrpol.bsd.on C6H6 (from parm99.dat) # X-CA-CA-X 330.33400 0.0 -30.33400 0.0 0.0 0.0 ; intrpol.bsd.on C6H6 --- I have no problems with the parameters for proteins. But, in case of the GLYCAM parameters, I am a little confused about the conversion of dihedral force constants (DFC), especially when the DFC and the periodicity values are 0 for example for this torsion: O2-P -OS-CP 10.10 0.0-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 Thank you in advance, for your help SA -- 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
Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.
On 19/07/2011 11:56 PM, sa wrote: Dear GROMCS users, I am trying to convert some GLYCAM parameters in GROMACS format. For this purpose, I am using the latest GLYCAM parameters downloaded from the RJ. Woods' website and the examples given in the acpype code (here for the dihedral angles) : http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 --- # dihedralidivfbarrier hight/2 kcal/mol phase degrees periodicity comments X -ca-ca-X4 14.500* 180.000 2.000 intrpol.bsd.on C6H6 * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in topolbuild, why?) = 30.334 or 15.167 kJ/mol # X -CA-CA-X4 14.50180.0 2.intrpol.bsd.on C6H6 (from parm99.dat) # X-CA-CA-X 330.33400 0.0 -30.33400 0.0 0.0 0.0 ; intrpol.bsd.on C6H6 --- I have no problems with the parameters for proteins. But, in case of the GLYCAM parameters, I am a little confused about the conversion of dihedral force constants (DFC), especially when the DFC and the periodicity values are 0 for example for this torsion: O2-P -OS-CP10.100.0-3.Dimethyl phosphate 1-0.500.0-2. 10.100.01 Where only a positive value makes sense, sometimes people use negative values to indicate some special functional form. This can be easier to code. Regardless, you'll have to check out the GLYCAM documentation and see what is meant, before you can address how to convert it into a GROMACS format. Obviously the contents of parts of chapter 4 and 5 of the manual will be important. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.
It is normal to have combinations of negative and positive values for the barrier heights. Those are just the best coefficients to reproduce some QM rotational energy curve during the parameterization. The negative periodicities are a convention from AMBER. They simply indicate that the dihedral angle potential has more than one term. For your example below: O2-P -OS-CP 1 0.10 0.0 -3. Dimethyl phosphate 1 -0.50 0.0 -2. 1 0.10 0.0 1 -3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive value is reached, terms for the O2-P-OS-CP potential have been completely accounted for. Hope that helps. Austin- --- On Tue, 7/19/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format. To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, July 19, 2011, 7:08 AM On 19/07/2011 11:56 PM, sa wrote: Dear GROMCS users, I am trying to convert some GLYCAM parameters in GROMACS format. For this purpose, I am using the latest GLYCAM parameters downloaded from the RJ. Woods’ website and the examples given in the acpype code (here for the dihedral angles) : http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9r=9redir=1 --- # dihedral idivf barrier hight/2 kcal/mol phase degrees periodicity comments X -ca-ca-X 4 14.500* 180.000 2.000 intrpol.bsd.on C6H6 * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in topolbuild, why?) = 30.334 or 15.167 kJ/mol # X -CA-CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 (from parm99.dat) # X-CA-CA-X 3 30.33400 0.0 -30.33400 0.0 0.0 0.0 ; intrpol.bsd.on C6H6 --- I have no problems with the parameters for proteins. But, in case of the GLYCAM parameters, I am a little confused about the conversion of dihedral force constants (DFC), especially when the DFC and the periodicity values are 0 for example for this torsion: O2-P -OS-CP 1 0.10 0.0 -3. Dimethyl phosphate 1 -0.50 0.0 -2. 1 0.10 0.0 1 Where only a positive value makes sense, sometimes people use negative values to indicate some special functional form. This can be easier to code. Regardless, you'll have to check out the GLYCAM documentation and see what is meant, before you can address how to convert it into a GROMACS format. Obviously the contents of parts of chapter 4 and 5 of the manual will be important. Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.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
Re: [gmx-users] conversion of gromacs files to amber files
I suppose it depends on what kind of analysis you would like to do... I'm not aware of any scripts for converting back from gmx into amber trajectories but I have done this before when doing an mmpbsa calculation using ambertools. As I only needed snaphots of the trajectory and not energies or velocities I used trajconv to write out pdb's for each timeframe I wanted then used a script to change the pdb's so that the atom names were compatible with amber. I then used ptraj to merge them into one crd file. Each case requires special attention though and it is cumbersome and time consuming. If you really need to do this I can share the script with you but I strongly recommend you either find a way to do the analysis with gmx or re-run the simulation with amber. Oliver On 7 December 2010 07:08, leila karami karami.lei...@gmail.com wrote: Dear gromacs users I did simulation of protein-dna by gromacs and amber03 force field. I want to do some analysis by amber. what is the best way for conversion of gromacs trajectory and topology files to amber files? any help will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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
[gmx-users] conversion of gromacs files to amber files
Dear Oliver Grant thanks for your attention. I want to use amber tool for hydrogen bond analysis especially (water mediated hydrogen bonds and residence time and occupation of them). -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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
Re: [gmx-users] conversion of gromacs files to amber files
Hi Leila, I've done this with g_hbond and g_bond. If you search the forums there is a perl script available from Justin Lemakul that will do this for you. You can do it manually too if you have only a few to look at. Its a little tricky but a lot easier than traj conversion. :) I was able to get % residence, average bond length and std dev of length but I had to use ndx files with just the 3 atoms in them. It's tedious so if you have a lot of bonds check out the perl script. Oliver On 7 December 2010 10:56, leila karami karami.lei...@gmail.com wrote: Dear Oliver Grant thanks for your attention. I want to use amber tool for hydrogen bond analysis especially (water mediated hydrogen bonds and residence time and occupation of them). -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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
[gmx-users] conversion of gromacs files to amber files
Dear Oliver very thanks for your help. Justin's perl script is good for direct hydrogen bonds, while I want to study water mediated hydrogen bonds and residence time and occupation of them. Are youe sure g_hbond give you residence time of hydrogen bonds? before you said you used a script to change the pdb file for compatibility with amber. please share me that. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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
Re: [gmx-users] conversion of gromacs files to amber files
You can try using vmd. It has a powerful language selection and it can be used remotely. There is one disadvantage: the trajectory MUST fit into memory since vmd loads the trajectory into memory. If this is not the case, you can use the script bigdcd that permits to load one frame in memory, analyzing it and then removing it from the memory. Then the next frame is loaded and the cicle start again. Dear gromacs users I did simulation of protein-dna by gromacs and amber03 force field. I want to do some analysis by amber. what is the best way for conversion of gromacs trajectory and topology files to amber files? any help will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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
Re: [gmx-users] conversion of gromacs files to amber files
Hi Leila, I would try the other suggested options like catdcd or vmd. The script is a pain and you would have to adapt it to work with DNA. It cost me a lot of time. I used g_hbond for residence time like this: g_hbond -f 8_fullMD_CA.xtc -s 7_fullMD.tpr -n g_hbond.ndx -a 170 -num g_hbond.log //the tpr file can't have restraints in it for some reason, thats why it is 7 and not 8. // ndx file has the 3 atoms in the hbond Checking for overlap in atoms between 0SA and SER Calculating hydrogen bonds between 0SA (1 atoms) and SER (2 atoms) Found 1 donors and 2 acceptors Will do grid-seach on 16x16x16 grid, rcut=0.35 Average number of hbonds per timeframe 0.872 out of 1 possible // so here's the % residence I found which residues were involved in hbonding to my ligand with an initial g_hbond run. I think you can get all the info you need from g_hbond. Oliver On 7 December 2010 11:37, leila karami karami.lei...@gmail.com wrote: Dear Oliver very thanks for your help. Justin's perl script is good for direct hydrogen bonds, while I want to study water mediated hydrogen bonds and residence time and occupation of them. Are youe sure g_hbond give you residence time of hydrogen bonds? before you said you used a script to change the pdb file for compatibility with amber. please share me that. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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
[gmx-users] conversion of gromacs files to amber files
Dear gromacs users I did simulation of protein-dna by gromacs and amber03 force field. I want to do some analysis by amber. what is the best way for conversion of gromacs trajectory and topology files to amber files? any help will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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
Re: [gmx-users] conversion of desmond trajectory files into gromacs
Really? This is really great! Is there any need to specify the location of the vmd libraries? If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this somehow still possible? On Apr 16, 2010, at 10:07 PM, Roland Schulz wrote: In case you use the GIT version of the analysis tools you don't need to convert the trajectories first. I've added that the analysis tools can read all vmd supported file formats if GROMACS finds the vmd libraries. Roland On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole x.peri...@rug.nl wrote: Well I guess you want to use gmx analysis tools so you'll have to build the gmx topology of your system when necessary! Often only a pdb file or a gro file is sufficient. On Apr 16, 2010, at 5:24 PM, ram bio wrote: Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- 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! 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/mailing_lists/users.php -- 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! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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! 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/mailing_lists/users.php -- 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! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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! 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/mailing_lists/users.php -- 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! 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/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
On Sat, Apr 17, 2010 at 7:54 AM, XAvier Periole x.peri...@rug.nl wrote: Really? This is really great! Is there any need to specify the location of the vmd libraries? By default it tries to find them at /usr/local/lib/vmd/plugins/*/molfile If you have them installed somewhere else you can specify it by setting the VMD_PLUGIN_PATH environment variable. If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this somehow still possible? It would be pretty simple to add, that one can read this molecule information also from pdb or from psf. But I didn't have time to do it. In case you are interested to do that, I can give you help doing it. Until someone implements it, one still needs the tpr file. For cases where it is difficult to generate a top file we have a version of psfgen which generates a top file from a psf. But we don't have solved the license issue so far (NAMD license) and thus can't provide this version yet. Roland On Apr 16, 2010, at 10:07 PM, Roland Schulz wrote: In case you use the GIT version of the analysis tools you don't need to convert the trajectories first. I've added that the analysis tools can read all vmd supported file formats if GROMACS finds the vmd libraries. Roland On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole x.peri...@rug.nl wrote: Well I guess you want to use gmx analysis tools so you'll have to build the gmx topology of your system when necessary! Often only a pdb file or a gro file is sufficient. On Apr 16, 2010, at 5:24 PM, ram bio wrote: Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- 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! 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/mailing_lists/users.php -- 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! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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! 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/mailing_lists/users.php -- 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! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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! 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/mailing_lists/users.php -- 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! 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/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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! 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/mailing_lists/users.php
[gmx-users] conversion of desmond trajectory files into gromacs
Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- 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! 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/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- 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! 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/mailing_lists/users.php -- 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! 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/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- gmx-users mailing list gmx-us...@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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! 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/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
Well I guess you want to use gmx analysis tools so you'll have to build the gmx topology of your system when necessary! Often only a pdb file or a gro file is sufficient. On Apr 16, 2010, at 5:24 PM, ram bio wrote: Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- 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! 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/mailing_lists/users.php -- 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! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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! 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/mailing_lists/users.php -- 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! 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/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
In case you use the GIT version of the analysis tools you don't need to convert the trajectories first. I've added that the analysis tools can read all vmd supported file formats if GROMACS finds the vmd libraries. Roland On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole x.peri...@rug.nl wrote: Well I guess you want to use gmx analysis tools so you'll have to build the gmx topology of your system when necessary! Often only a pdb file or a gro file is sufficient. On Apr 16, 2010, at 5:24 PM, ram bio wrote: Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- 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! 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/mailing_lists/users.php -- 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! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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! 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/mailing_lists/users.php -- 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! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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! 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/mailing_lists/users.php
[gmx-users] conversion between harmonic bonds/angles and GROMOS96 bonds/angles
I am interested in converting between GROMOS96 bond/angle potentials and standard harmonic potentials. The GROMACS manual (version 4) suggests formulae for doing so (Eq. 4.38 and Eq. 4.53). However, I am having trouble understanding where these come from and find that they seem to give rather poor approximations for the conversions. It seems that much more accurate (but somewhat more complex) conversion expressions can be derived but I am wondering whether I do not fully understand the GROMOS96 bond potentials vs. standard harmonic potentials. Any insights? Thanks, Michael. -- 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! 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/mailing_lists/users.php
[gmx-users] Conversion
Dear gromacs users, How can I convert a certain concentration of a compound (say in mg/ml) to be used in my simulations, into number of molecules to be added in the system??? Please help. See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/___ 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! 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/mailing_lists/users.php
Re: [gmx-users] Conversion
P.R.Anand Narayanan wrote: Dear gromacs users, How can I convert a certain concentration of a compound (say in mg/ml) to be used in my simulations, into number of molecules to be added in the system??? Basic general chemistry: from mg/mL to molarity, then to number of molecules per unit volume. -Justin Please help. See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz http://in.rd.yahoo.com/tagline_buzz_1/*http://in.buzz.yahoo.com/. ___ 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! 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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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! 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/mailing_lists/users.php
[gmx-users] Conversion of units to nm in .xyz or pdb
hello gromacs users, I am working with a silica structure which is parallepiped in structure, i.e the unit cell is 46.4207 37.7846 18.9596 angles =90, 90, 120 I have a structure file in .xyz and .pdb but the units are in Angstroms and for gromacs I assume that I need to convert these units to nm? This is where I am encountering problems. I have tried simply dividing the atomic coordinates and cell lengths by a factor of 10 but the resulting structure doesnt look right in vmd. Do I need to use some sort of symmetry transformation to take the non-cubic symmetry into account when scaling the coordinates? Is there some program (either within gromacs or external) which will convert atomic coordinates from Angstroms to nm while carrying out the necessary symmetry operations? Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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! 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/mailing_lists/users.php
Re: [gmx-users] Conversion of units to nm in .xyz or pdb
Jennifer Williams wrote: hello gromacs users, I am working with a silica structure which is parallepiped in structure, i.e the unit cell is 46.4207 37.7846 18.9596 angles =90, 90, 120 I have a structure file in .xyz and .pdb but the units are in Angstroms and for gromacs I assume that I need to convert these units to nm? This is where I am encountering problems. You do not need to make any conversion. Gromacs can handle .pdb files just fine. I have tried simply dividing the atomic coordinates and cell lengths by a factor of 10 but the resulting structure doesnt look right in vmd. Do I need to use some sort of symmetry transformation to take the non-cubic symmetry into account when scaling the coordinates? Is there some program (either within gromacs or external) which will convert atomic coordinates from Angstroms to nm while carrying out the necessary symmetry operations? Simply dividing by 10 may have altered the formatting of your file. There are certain formatting standards that must be adhered to in structure files. But as I said above, .pdb format is just fine. -Justin Thanks -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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! 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/mailing_lists/users.php
[gmx-users] conversion to tip5p
Hi, all Using gromacs 3.3 I try to work with tip5 water, but I fail to convert water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is easy with pdb2gmx pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top , but when I apply similar command for tip5p, the output gro-file contains only four-point water molecules. Could anyone help me? -- Regards, Dmitri mailto:ddu...@ngs.ru___ 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! 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/mailing_lists/users.php
Re: [gmx-users] conversion to tip5p
2009/6/5 Dmitri Dubov ddu...@ngs.ru Hi, all Using gromacs 3.3 I try to work with tip5 water, but I fail to convert water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is easy with pdb2gmx pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top Does it really converts like that? I mean will it adjust the bonds and add a dummy atom just like that? , but when I apply similar command for tip5p, the output gro-file contains only four-point water molecules. Could anyone help me? -- Regards, Dmitri mailto:ddu...@ngs.ru ddu...@ngs.ru ___ 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! 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/mailing_lists/users.php Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ 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! 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/mailing_lists/users.php
Re: [gmx-users] conversion to tip5p
Dmitri Dubov wrote: Hi, all Using gromacs 3.3 I try to work with tip5 water, but I fail to convert water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is easy with pdb2gmx pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top , but when I apply similar command for tip5p, the output gro-file contains only four-point water molecules. Could anyone help me? Upgrade to gromacs-4.0.5; what you want to do works for me. -Justin -- Regards, Dmitri mailto:ddu...@ngs.ru ___ 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! 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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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! 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/mailing_lists/users.php
Re: [gmx-users] Conversion of trajectories to netcdf format
I don't know about netcdf, but you can use wordom to convert from xtc to dcd. Contact me off list if you don't succeed - I'm not sure whether the online documentation of wordom is up-to-date. Ran. Tobias Unruh wrote: Hi, I would like to use nMolDyn for the analysis of the GROMACS trajectories. I tried VMD and catdcd to convert trr/tpr files to dcd/pdb files. But the conversion of the dcd/pdb files to nc (netcdf) files using the dcd_to_nc program of the nMolDyn package does not work. Obviously the header of the dcd file differs from what is expected by the dcd_to_nc program which uses MMTK. Does anyone know how to convert the GROMACS trajectories such that nMolDyn can be used for calculation of correlation and intermediate scattering functions? I appreciate any suggestion. Regards Tobias -- Tobias Unruh TU Muenchen, FRM-II 85747 Garching, Germany ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Conversion of trajectories to netcdf format
Hi, I would like to use nMolDyn for the analysis of the GROMACS trajectories. I tried VMD and catdcd to convert trr/tpr files to dcd/pdb files. But the conversion of the dcd/pdb files to nc (netcdf) files using the dcd_to_nc program of the nMolDyn package does not work. Obviously the header of the dcd file differs from what is expected by the dcd_to_nc program which uses MMTK. Does anyone know how to convert the GROMACS trajectories such that nMolDyn can be used for calculation of correlation and intermediate scattering functions? I appreciate any suggestion. Regards Tobias -- Tobias Unruh TU Muenchen, FRM-II 85747 Garching, Germany ___ gmx-users mailing listgmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] conversion?
Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply Thanks in advance.___ gmx-users mailing listgmx-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] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] conversion?
minnale wrote: Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply The *exact* same question was asked yesterday: http://www.gromacs.org/pipermail/gmx-users/2008-September/036332.html ...with subsequent replies this morning. Do check the list archive for solutions, and keep an eye on (at least) the subject lines of the emails to the list. Every once in a while, one may come across that is of interest to you :) -Justin Thanks in advance. Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201650/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-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] 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 | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] conversion?
thanks alot Justin for your reply On Tue, 09 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply The *exact* same question was asked yesterday: http://www.gromacs.org/pipermail/gmx-users/2008-September/036332.html ...with subsequent replies this morning. Do check the list archive for solutions, and keep an eye on (at least) the subject lines of the emails to the list. Every once in a while, one may come across that is of interest to you :) -Justin Thanks in advance. Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201650/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-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] 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 | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] conversion of xtc to g87 (amber) format trajectory files/bounding box problem?
Hi everyone I'd like to convert my Gromacs trajectory to an Amber format for use with the CAVER program. Reading round, it seems that Amber is equivalent to the g87 format so I can use trjconv to produce the file. This all seems to work well (the file gets read in and processed) except for a problem with the bounding box. When caver works on a PDB file and generates its own box it comes out like this Grid: [63 82 76] BBox: (39.198000 6.232000 19.088000 ,89.027000 71.759000 79.758000 ) The box that gets read from the g87 trajectory looks like this Grid: [7 9 7] BBox: (3.307000 0.906000 1.856000 ,8.843000 7.67 7.336000 ) From other reading there seems to be a unit issue (A vs nm) in the Gromacs/Amber comparison. The two boxes above are quite close to 10-fold different in all dimensions. Is this the source of my problem? How can I work around this? Thanks in advance for your help Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. ___ gmx-users mailing listgmx-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] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] conversion gromos gromacs
Hi, I need to convert GROMOS topology file into GROMACS format, I wonder if someone know of a program in GROMACS or GROMOS packages that does it. Thanks, Itamar -- Prediction is very difficult, especially about the future - Niels Bohr ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
