[gmx-users] error in residue topology

[Mark Abraham]

Chanchal wrote:
> Hi Justin,
>   Thanks for the info. I know that the topologies are provided in that
> website.  But they have used charmm27 ff and converted it to gromacs format.
> But I want to use gromos96 45a3 ff.

Does that force field support sugar/membrane interactions? Can it model 
sugars separately, and membranes separately? Is there evidence the 
combination might also work?

> I have another question. Suppose I use those topologies for dopc . And for
> the sugar part, I use gromos96 45a3. Will it create problem when we combine
> sugar /dopc system?

Yes. See http://oldwiki.gromacs.org/index.php/Force_Fields

Mark

> Thanks
> Chanchal
> 
> On Tue, Aug 18, 2009 at 7:46 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 
>>
>> Chanchal wrote:
>>
>>> Hi All,
>>>   I am a novice in gromacs. I want to study sugar/membrane interaction and
>>> I want to use gromos96 45a3 ff. At first  I am planning to simulate  dopc
>>>  bilayer + water.  I downloaded the pdb file of dopc  from the site
>>> http://www.bioinf.uni-sb.de/RB/ .  Then I typed pdb2gmx_d -f dopc.pdb and
>>> choose gromos96 45a3 force field. But I got the error "Residue 'OLE' not
>>> found in residue topology database". How can I fix the error?
>>>
>> This happens because pdb2gmx is not magic.  See here:
>>
>>
>> http://oldwiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
>>
>> The website you reference provides suitable topologies for this type of
>> simulation, making pdb2gmx unnecessary.
>>
>> -Justin
>>
>>  Thanks
>>> Chanchal
>>>
>>>
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>> --
>> ========================================
>>
>> 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
>>
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> 
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