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<div>I think the Ausi ATB is a bit beter for initial topologies,but still needs some input afterwards. They usually have less to change around needed, or beter charge sets, but tend to have problems with adding a hydrogen. Only for 53a6 though. Also, just loking at the ff topoloy you canput one together from scratch from what is already in gromacs, but painfull...there are a large amunt of MD's with all atom or berger lipids in a 53a6 which should work with a7 as well, and the ATB has a few constructed all or UA lipids, cholestorols on its site already done...</div>
<div> </div>
<div>My opinion,</div>
<div> </div>
<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Donnerstag, 29. Mai 2014 um 16:55 Uhr<br/>
<b>Von:</b> "Todor Antonijevic" <t_antoni@uncg.edu><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> Re: [gmx-users] New Molecule Topology</div>
<div name="quoted-content">Hi Justin,<br/>
<br/>
Thank you for you answer.<br/>
It sounds to me that using PRODRG server for the initial topology and then<br/>
correcting atom types and other parameters according to Berger lipids is<br/>
acceptable method.<br/>
<br/>
What about "constructing" cholesteryl oleate molecule by "gluing" together<br/>
known cholesterol force field with oleate chain taken from POPC?<br/>
<br/>
Thank you in advance,<br/>
<br/>
Anton<br/>
<br/>
<br/>
On Wed, May 28, 2014 at 8:33 PM, Justin Lemkul <jalemkul@vt.edu> wrote:<br/>
<br/>
><br/>
><br/>
> On 5/28/14, 1:33 PM, Todor Antonijevic wrote:<br/>
><br/>
>> Hi,<br/>
>><br/>
>> I would like to create a topology file for cholesteryl oleate molecule.<br/>
>> Is it a good practice to use PRODRG server to generate all connections,<br/>
>> and<br/>
>> then to change atom types and parameters according to the Berger force<br/>
>> field?<br/>
>><br/>
>> Is there a better approach?<br/>
>><br/>
>><br/>
> No matter how you produce the initial topology (PRODRG, ATB, etc), you'll<br/>
> likely end up gutting nearly the entire topology to replace the atom types,<br/>
> charges, and bonded parameters.<br/>
><br/>
> -Justin<br/>
><br/>
> --<br/>
> ==================================================<br/>
><br/>
> Justin A. Lemkul, Ph.D.<br/>
> Ruth L. Kirschstein NRSA Postdoctoral Fellow<br/>
><br/>
> Department of Pharmaceutical Sciences<br/>
> School of Pharmacy<br/>
> Health Sciences Facility II, Room 601<br/>
> University of Maryland, Baltimore<br/>
> 20 Penn St.<br/>
> Baltimore, MD 21201<br/>
><br/>
> jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br/>
> <a href="http://mackerell.umaryland.edu/~jalemkul" target="_blank">http://mackerell.umaryland.edu/~jalemkul</a><br/>
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