[gmx-users] GROMOS54A8 parameters in GROMACS format
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Thu Feb 14 15:05:19 CET 2013
Thanks Berk,
I have found the script, I will try them
Best
Stephane
----------------------------------------
Message: 4
Date: Thu, 14 Feb 2013 13:53:56 +0100
From: Berk Hess <gmx3 at hotmail.com>
Subject: RE: [gmx-users] Re: GROMOS54A8 parameters in GROMACS format
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <DUB124-W200B8C2EB085C78933A9418E0F0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
There are two scripts make_gromos_rtp in the scripts directory which were used to convert Gromos AA topologies to rtp entries.
Cheers,
Berk
----------------------------------------
> From: Stephane.ABEL at cea.fr
> To: gmx-users at gromacs.org
> Date: Thu, 14 Feb 2013 11:34:59 +0000
> Subject: [gmx-users] Re: GROMOS54A8 parameters in GROMACS format
>
> Hello,
>
> Yeap, I have seen the links on ATB. Indeed, the conversion of the bonded terms (in this file 54a8.ifp ?) will be not too hard, but it is not the case for the AA topology where several changes were done.
>
> So any help will be appreciate..
>
> Stephane
>
> ------------------------------
>
> Message: 5
> Date: Thu, 14 Feb 2013 11:18:17 +0100
> From: "lloyd riggs" <lloyd.riggs at gmx.ch>
> Subject: Re: [gmx-users] GROMOS54A8 parameters in GROMACS format
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <20130214101817.72310 at gmx.net>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Stephane Abel,
>
> Theres a link I on the gromacs web site to ATB, or you can google it. If it is not in Gromacs format you can just write a couple 6 liner scripts to re-format it by parsing into the gromacs format,
>
> Stephan Watkins
>
> -------- Original-Nachricht --------
> > Datum: Wed, 13 Feb 2013 21:25:33 +0000
> > Von: ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
> > An: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> > Betreff: [gmx-users] GROMOS54A8 parameters in GROMACS format
>
> > Hello all,
> >
> > Does somebody know where i can find the latest GROMOS force field (i.e.
> > GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ?
> >
> > [1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247???1264 doi:
> > http://pubs.acs.org/doi/citedby/10.1021/ct300156h
> >
> > Thank you
> >
> > Stephane
>
>
> ------------------------------
>
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Message: 5
Date: Thu, 14 Feb 2013 08:01:43 -0500
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] different springs - WHAM
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <511CE037.5020900 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2/13/13 5:23 PM, Steven Neumann wrote:
> On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 2/12/13 9:57 AM, Steven Neumann wrote:
>>>
>>> On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>> On 2/12/13 9:40 AM, Steven Neumann wrote:
>>>>>
>>>>>
>>>>> Dear Gmx Users,
>>>>>
>>>>> I know it is possible to combine windows with different spring
>>>>> constants into the one PMF curve using g_wham.
>>>>>
>>>>> Do I have to somehow tell g_wham that one or two windows have
>>>>> different spring constants?
>>>>>
>>>>
>>>> No, they are read from the .tpr files.
>>>>
>>>>
>>>>> For instance - I got the better histogram overlap with lower force
>>>>> constant in one window. When I replace this window into the window
>>>>> with the sring constant like all windwos (worse overlap) both PMF
>>>>> curves differ app. 2kcal/mol which is around 30% of the overall
>>>>> deltaG.
>>>>>
>>>>> Is there any error I should inroduce when one window differ in terms of
>>>>> k1?
>>>>>
>>>>
>>>> What does g_wham's error analysis suggest?
>>>>
>>>> -Justin
>>>
>>>
>>> In both PMF error estimate with bayesian bootstraping is app. 0.2 kcal/mol
>>>
>>
>> Seems like a good result, so what's the problem?
>>
>> -Justin
>
> That the better overlap of histograms produce worse deltaG comparing
> to experiment. With all the same spring constants I get the
> experimental value of deltaG but there is a poor overlap. There must
> be (somehow) a correction added to deltaG when introdcuing windows
> with different spring constants.
>
The code and/or g_wham paper should address this. In principle, WHAM can be
conducted with any assortment of spring constants you like. If you track down a
bug or something, please report it on redmine.gromacs.org.
A workaround of course would be to simply add another window (or windows) with
the same original force constant that gives adequate sampling.
-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
========================================
------------------------------
Message: 6
Date: Thu, 14 Feb 2013 08:03:28 -0500
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Implicit solvent
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <511CE0A0.8040705 at vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
On 2/14/13 1:01 AM, ?????????????? ???????????????? wrote:
> Hi, dear developers!
>
> I want to ask you abou dynamics in implicit solvent. I have a complex of
> animal protein - dimer/trimer. After modeling by homology I have built
> another one from the plant organism. Dimer/trimer was constructed with
> superposition method. The question is - can I use imlicit solvent model to
> optimize and relax this complex? Is it real and where I can find suitable
> parameters of mdp?
>
Infinite cutoffs with a nonperiodic unit cell are generally advisable for
running implicit solvent calculations. They don't parallelize well due to a bug
that I believe is still being fixed, so you can only run on 1-2 processors in
implicit solvent. Performance for large systems actually scales better in
explicit solvent, especially if you use GPU acceleration.
-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
========================================
------------------------------
Message: 7
Date: Thu, 14 Feb 2013 08:04:51 -0500
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] md with multiple ligands
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <511CE0F3.8000502 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2/14/13 1:20 AM, Ansuman Biswas wrote:
> ---------------------------- Original Message ----------------------------
> Subject: Re: gmx-users Digest, Vol 106, Issue 68
> From: ansuman at localhost
> Date: Thu, February 14, 2013 10:16 am
> To: gmx-users at gromacs.org
> --------------------------------------------------------------------------
>
>
>>
>> Message: 8
>> Date: Wed, 13 Feb 2013 08:28:00 -0500
>> From: Justin Lemkul <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] md with multiple ligands
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <511B94E0.4040800 at vt.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>>
>> On 2/13/13 5:24 AM, Ansuman Biswas wrote:
>>>
>>> Dear gromacs users,
>>>
>>> I wish to run a protein ligand md in Gromacs 4.5.3 with charmm force
>>> field. Its a dimeric protein with a MG ion and 2 ligands bound to two
>>> active sites. I wish to run the dimer and there would be 4 ligands. I
>>> generated the topology files (.itp) of ligands using SWISSPARAM. Before
>>> running the energy minimization I changed the topol.top file accordingly
>>> as mentioned in the SWISSPARAM website. I added all the itp files
>>> together.But while running GROMPP I got an error message like,
>>>
>>>
>>> WARNING 1 [file ADP.itp, line 24]:
>>> Overriding atomtype NPYL
>>>
>>>
>>> WARNING 2 [file ADP.itp, line 25]:
>>> Overriding atomtype C5A
>>>
>>>
>>> WARNING 3 [file ADP.itp, line 26]:
>>> Overriding atomtype N5B
>>>
>>>
>>> WARNING 4 [file ADP.itp, line 27]:
>>> Overriding atomtype C5B
>>>
>>>
>>> WARNING 5 [file ADP.itp, line 28]:
>>> Overriding atomtype CB
>>>
>>>
>>> WARNING 6 [file ADP.itp, line 29]:
>>> Overriding atomtype NPYD
>>>
>>>
>>> WARNING 7 [file ADP.itp, line 30]:
>>> Overriding atomtype PO4
>>>
>>>
>>> WARNING 8 [file ADP.itp, line 31]:
>>> Overriding atomtype O2CM
>>>
>>>
>>> WARNING 9 [file ADP.itp, line 32]:
>>> Overriding atomtype OR
>>>
>>>
>>> WARNING 10 [file ADP.itp, line 33]:
>>> Overriding atomtype CR
>>>
>>>
>>> WARNING 11 [file ADP.itp, line 34]:
>>> Overriding atomtype NC=C
>>>
>>>
>>> WARNING 12 [file ADP.itp, line 35]:
>>> Overriding atomtype HCMM
>>>
>>>
>>> WARNING 13 [file ADP.itp, line 36]:
>>> Overriding atomtype HNCO
>>>
>>>
>>> WARNING 14 [file ADP.itp, line 37]:
>>> Overriding atomtype HOCO
>>>
>>>
>>> WARNING 15 [file ADP.itp, line 38]:
>>> Overriding atomtype HOR
>>>
>>>
>>> WARNING 16 [file ADP.itp, line 43]:
>>> Overriding atomtype PO4
>>>
>>>
>>> WARNING 17 [file ADP.itp, line 44]:
>>> Overriding atomtype O2CM
>>>
>>>
>>> WARNING 18 [file ADP.itp, line 45]:
>>> Overriding atomtype OR
>>>
>>>
>>> WARNING 19 [file ADP.itp, line 46]:
>>> Overriding atomtype CR
>>>
>>>
>>> WARNING 20 [file ADP.itp, line 48]:
>>> Overriding atomtype HCMM
>>>
>>>
>>> WARNING 21 [file ADP.itp, line 49]:
>>> Overriding atomtype HOR
>>>
>>>
>>> WARNING 22 [file ADP.itp, line 50]:
>>> Overriding atomtype HOCO
>>>
>>>
>>> WARNING 23 [file ADP.itp, line 52]:
>>> Overriding atomtype NC=O
>>>
>>>
>>> WARNING 24 [file ADP.itp, line 53]:
>>> Overriding atomtype C=O
>>>
>>>
>>> WARNING 25 [file ADP.itp, line 54]:
>>> Overriding atomtype N=C
>>>
>>>
>>> WARNING 26 [file ADP.itp, line 55]:
>>> Overriding atomtype C=C
>>>
>>>
>>> WARNING 27 [file ADP.itp, line 56]:
>>> Overriding atomtype PO4
>>>
>>>
>>> WARNING 28 [file ADP.itp, line 57]:
>>> Overriding atomtype O2CM
>>>
>>>
>>> WARNING 29 [file ADP.itp, line 58]:
>>> Overriding atomtype OR
>>>
>>>
>>> WARNING 30 [file ADP.itp, line 59]:
>>> Overriding atomtype CR
>>>
>>>
>>> WARNING 31 [file ADP.itp, line 60]:
>>> Overriding atomtype O=C
>>>
>>>
>>> WARNING 32 [file ADP.itp, line 61]:
>>> Overriding atomtype HCMM
>>>
>>>
>>> WARNING 33 [file ADP.itp, line 62]:
>>> Overriding atomtype HOCO
>>>
>>>
>>> WARNING 34 [file ADP.itp, line 63]:
>>> Overriding atomtype HOR
>>>
>>>
>>> WARNING 35 [file ADP.itp, line 64]:
>>> Overriding atomtype HOCC
>>>
>>> Generated 25425 of the 25425 non-bonded parameter combinations
>>> Generating 1-4 interactions: fudge = 1
>>> Generated 22285 of the 25425 1-4 parameter combinations
>>>
>>> -------------------------------------------------------
>>> Program grompp, VERSION 4.5.3
>>> Source code file: toppush.c, line: 1071
>>>
>>> Fatal error:
>>> Atoms in the .top are not numbered consecutively from 1 (rather, atomnr
>>> =
>>> 1, while at->nr = 40)
>>>
>>> I know that the problem is related to the merging of 4 itp files.
>>> Please let me how I should do that.
>>>
>>
>> The ligands probably use common atom types and each .itp file likely has
>> an
>> [atomtypes] directive that introduces these new types. Probably the
>> easiest
>> thing to do is create a merged [atomtypes] directive that lists all of the
>> necessary atom types so you don't list them separately in each file. One
>> approach that I have used in the past is to create an .itp file that only
>> has
>> atom types in it, then call something like:
>>
>> #include "charmm27.ff/forcefield.itp"
>>
>> ; only has [atomtypes]
>> #include "my_ligand_atomtypes.itp"
>>
>> ; these don't introduce [atomtypes] any more
>> #include "ligand1.itp"
>> #include "ligand2.itp"
>>
>> -Justin
> But according to SWISSPARAM website I can only add one ligand.itp file.
Just a guess, but it's probably because each ligand.itp file introduces new atom
types which give the conflicts above.
> So, is it possible to add ligand1 and ligand2 itp files?
>
Sure, my method should work. Please try it. I have done the exact same thing
with Amber topologies from acpype.
> Will it be ok if I merge all the ligand pdbs and then get the combined itp
> file using that from SWISSPARAM and follow the protocol for one ligand?
>
Merging the coordinate files will probably not work. If you have multiple
molecules, you need multiple topologies.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
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