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 <g...@hotmail.com>
Subject: RE: [gmx-users] Re: GROMOS54A8 parameters in GROMACS format
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <dub124-w200b8c2eb085c78933a9418e...@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.a...@cea.fr
> To: gmx-users@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.ri...@gmx.ch>
> Subject: Re: [gmx-users] GROMOS54A8 parameters in GROMACS format
> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Message-ID: <20130214101817.72...@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.a...@cea.fr>
> > An: "gmx-users@gromacs.org" <gmx-users@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
>
>
> ------------------------------
>
> --
> 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!
>
> End of gmx-users Digest, Vol 106, Issue 73
> ******************************************
> --
> 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


------------------------------

Message: 5
Date: Thu, 14 Feb 2013 08:01:43 -0500
From: Justin Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] different springs - WHAM
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <511ce037.5020...@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 <jalem...@vt.edu> wrote:
>>
>>
>> On 2/12/13 9:57 AM, Steven Neumann wrote:
>>>
>>> On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul <jalem...@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 <jalem...@vt.edu>
Subject: Re: [gmx-users] Implicit solvent
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <511ce0a0.8040...@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 <jalem...@vt.edu>
Subject: Re: [gmx-users] md with multiple ligands
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <511ce0f3.8000...@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@localhost
> Date:    Thu, February 14, 2013 10:16 am
> To:      gmx-users@gromacs.org
> --------------------------------------------------------------------------
>
>
>>
>> Message: 8
>> Date: Wed, 13 Feb 2013 08:28:00 -0500
>> From: Justin Lemkul <jalem...@vt.edu>
>> Subject: Re: [gmx-users] md with multiple ligands
>> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>> Message-ID: <511b94e0.4040...@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

========================================


------------------------------

--
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!

End of gmx-users Digest, Vol 106, Issue 74
******************************************
--
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

Reply via email to