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...
My opinion,
Stephan Watkins
Gesendet: Donnerstag, 29. Mai 2014 um 16:55 Uhr
Von: "Todor Antonijevic" <[email protected]>
An: [email protected]
Betreff: Re: [gmx-users] New Molecule Topology
Von: "Todor Antonijevic" <[email protected]>
An: [email protected]
Betreff: Re: [gmx-users] New Molecule Topology
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 <[email protected]> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> [email protected] | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
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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 <[email protected]> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> [email protected] | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to [email protected].
>
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