[gmx-users] how to build topology

[Victor Rosas Garcia]

darn it!  I was hoping the answer would be different. :(

Perhaps I can take the topology from acpype and tweak the atomtypes by
hand. Are there any caveats or potential traps in doing this?

Victor

2014-10-15 15:13 GMT-05:00 Dr. Vitaly Chaban <vvchaban at gmail.com>:
> I believe only writing the ITP file(s) by hand.
>
>
> Dr. Vitaly V. Chaban
>
> Виталий Витальевич ЧАБАН
>
>
> On Wed, Oct 15, 2014 at 5:49 PM, Victor Rosas Garcia
> <rosas.victor at gmail.com> wrote:
>> Hello everybody,
>>
>> I want to build a topology for a lipid to use the parameters reported
>> by Jämbeck and Lyubartsev
>>
>> Jämbeck, Joakim P. M., y Alexander P. Lyubartsev. «Derivation and
>> Systematic Validation of a Refined All-Atom Force Field for
>> Phosphatidylcholine Lipids». J. Phys. Chem. B 116, n.o 10 (2012):
>> 3164-79. doi:10.1021/jp212503e.
>>
>> but the modified forcefield provided by the authors is not included by
>> default in Gromacs (I am still using version 4.5.4).
>>
>> How could I build a topology that uses this modified forcefield?  I
>> have tried acpype, but it uses atomtypes different from the ones I
>> want.
>>
>> Best regards
>>
>> Victor
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