[gmx-users] charmmff

[Sai Pooja]

Hi,

So you mean it would be easier if one creates a topology file with all
parameters obtained from charmm forcefield?
Yes, makes a lot more sense than trying to change the software. Can you give
a little insight into the basic steps?

Pooja



On Wed, Jul 21, 2010 at 1:43 PM, Rodrigo Faccioli <
rodrigo_faccioli at uol.com.br> wrote:

> Hi,
>
> I've been developing an evolutionary algorithm which I would like to
> integrate it with Gromacs. Thus, in this moment, I'm updating my own code to
> attend the Gromacs patterns.
>
> Based on charmm27.ff directory I've built h files which contain some amino
> acids (ALA, GLY and ARG). I'm modelling my algorithm I'll put more amino.
> However, if you want to see my files, please see the main in [1].
>
> I create that file for mapping the files of charmm27.ff instead of work
> with .c files from pdb2gmx. Maybe if you create your charmm file mapping
> your job will be easier.
>
> [1]
> http://gitorious.org/protpred-gromacs/protpred-gromacs/blobs/master/include/topology_charmm27_parameters.h
>
> Thanks in advance,
>
>
> --
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL
> Intelligent System in Structure Bioinformatics
> http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
>
>
> On Wed, Jul 21, 2010 at 1:38 PM, Sai Pooja <saipooja at gmail.com> wrote:
>
>> Thanks Rodrigo. I have read the paper and and I am familiar with the
>> topology folder.
>> This is what I want to do:
>>
>> I have a version of gromacs without the charmm forcefield which I have
>> modified to use an algorithm I need.
>>
>> However, I now need to use charmm ff with this algorithm and in gromacs.
>>
>> It would be extremely tedious to modify another version of gromacs(with
>> charmm ff i.e.) for this algorithm. So , I was thinking if I could just copy
>> the top folder from a git version of gromacs(with charmmff) and make changes
>> in configure files to make it work with my version?
>>
>> Can someone give me some pointers on this? For example which files much be
>> changed/ modified?
>>
>> I have some thoughts:
>> 1. Clearly, the topology folder has been changed. It has new files on
>> charmm and the organization of files has also been changed --> cp topology
>> folder from git and put into my version
>>
>> 2. Make changes in configure.ac
>> The git version have extra commands for compiling top files for each
>> forcefield - copy those commands exactly from the git version and add to my
>> version.
>>
>> 3. I think that some files connected to pdb2gmx might have to be changed.
>> Which ones I am not sure. I am only interested in the .c files. Maybe
>> toppush.c?
>>
>> What else would I need to change? Any pointers would be very helpful.
>> Kindly let me know even if you have attempted something similar.
>>
>> Thanks
>> Pooja
>>
>> On Tue, Jul 20, 2010 at 8:14 PM, Rodrigo Faccioli <
>> rodrigo_faccioli at uol.com.br> wrote:
>>
>>> Hi,
>>>
>>> The gromacs version in git master, please see the directory
>>> share/top/charmm27.ff
>>>
>>> That directory contains whole gromacs charmm files. Furthermore, please
>>> see the reference below which explain more details about these parameters.
>>>
>>> Bjelkmar, Larsson, Cuendet, Hess, and Lindahl, JCTC 2010
>>>
>>> I hope those informations help you.
>>>
>>> What do you want to do more specific?
>>>
>>> --
>>> Rodrigo Antonio Faccioli
>>> Ph.D Student in Electrical Engineering
>>> University of Sao Paulo - USP
>>> Engineering School of Sao Carlos - EESC
>>> Department of Electrical Engineering - SEL
>>> Intelligent System in Structure Bioinformatics
>>> http://laips.sel.eesc.usp.br
>>> Phone: 55 (16) 3373-9366 Ext 229
>>> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
>>> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
>>>
>>>
>>> On Tue, Jul 20, 2010 at 6:57 PM, Sai Pooja <saipooja at gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> If one has to make a version of gromacs charmm compatible, which files
>>>> from the charmm compatible version must be looked at?
>>>>
>>>> Pooja
>>>>
>>>> --
>>>> Quaerendo Invenietis-Seek and you shall discover.
>>>>
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>>>
>>>
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>>
>>
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
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>
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-- 
Quaerendo Invenietis-Seek and you shall discover.
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