[gmx-users] Re: gmx-users Digest, Vol 92, Issue 66

[Rongliang Wu]

On 13/12/2011 11:46, gmx-users-request at gromacs.org wrote:
>
> Message: 1
> Date: Tue, 13 Dec 2011 17:10:01 +1100
> From: Mark Abraham<Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Force field for polymer molecule - tips
> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> Message-ID:<4EE6EC39.2090604 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 13/12/2011 5:06 PM, Jernej Zidar wrote:
>> Hi.
>>    I would like to use a CHARMM (CGennFF based) of polymer molecule in
>> Gromacs. The polymer is composed of three different monomer and two
>> different terminal residues (one for each of the the two terminals) -
>> five residues in total.
>>
>>    The CHARMM generalized FF has already been ported to Gromacs so
>> judging from the documentation
>> (http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field)
>> I should create a monomeres.rtp (arbitrary name?) file containing the
>> information about the monomeres. Any tips on doing that?
>>
>>    The general workflow will be:
>> Generate the initial structure of the polymer of a given composition
>> using Charmm* and save the coordinates as a PDB (plus two other
>> files). Then supply the generated PDB to pdb2gmx to generate the
>> initial GRO file.
>>
>>    Second question:
>> How will pdb2gmx "know" it has to parse the monomeres.rtp file?
> It can't. You must add to an existing .rtp file.
>
> Mark
>
I will add that you will also have to add the residue to aminoacids.dat 
file, so that the polymer repeat unit is recognized. for your small 
polymer molecule you can just generate from the swissparam website
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