[gmx-users] New Molecule Topology

[Todor Antonijevic]

Hi Justin,

Thank you for you answer.
It sounds to me that using PRODRG server for the initial topology and then
correcting atom types and other parameters according to Berger lipids is
acceptable method.

What about "constructing" cholesteryl oleate molecule by "gluing" together
known cholesterol force field with oleate chain taken from POPC?

Thank you in advance,

Anton


On Wed, May 28, 2014 at 8:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/28/14, 1:33 PM, Todor Antonijevic wrote:
>
>> Hi,
>>
>> I would like to create a topology file for cholesteryl oleate molecule.
>> Is it a good practice to use PRODRG server to generate all connections,
>> and
>> then to change atom types and parameters according to the Berger force
>> field?
>>
>> Is there a better approach?
>>
>>
> No matter how you produce the initial topology (PRODRG, ATB, etc), you'll
> likely end up gutting nearly the entire topology to replace the atom types,
> charges, and bonded parameters.
>
> -Justin
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
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> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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