[gmx-users] New Molecule Topology

[Todor Antonijevic]

Hi,

I've got very pleasant answer from ATB.

They provided me with a link for manually optimized topology of cholesterol
(GROMOS53A6): http://compbio.biosci.uq.edu.au/atb/molecule.py?molid=1731
and I have found manually optimized POPC topology (GROMOS54A7) :
http://compbio.biosci.uq.edu.au/atb/molecule.py?molid=1506

Now I have two question:

   1. May I combine cholesterol G53A6 topology with POPC taken from Prof.
   Tieleman's webpage in order to get cholesteryl oleate topology?
   2. What about combining cholesterol G53A6 with POPC G54A7 for the same
   purpose?

Thank you!


On Tue, Jun 3, 2014 at 5:47 PM, Todor Antonijevic <t_antoni at uncg.edu> wrote:

> Hi,
>
> I tried ATB but it has wrong database files. For example, Gromacs united
> atom .itp file is missing Carbon 28,29 and 30. I hope I will get help from
> them on this matter.
>
> Thank you
>
>
> On Fri, May 30, 2014 at 2:06 AM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:
>
>> 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" <t_antoni at uncg.edu>
>> *An:* gmx-users at gromacs.org
>> *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 <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
>> >
>> > --
>> > ==================================================
>> >
>> > 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
>> >
>> > jalemkul at outerbanks.umaryland.edu | (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 gmx-users-request at gromacs.org.
>> >
>> --
>> 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 gmx-users-request at gromacs.org.
>>
>> --
>> 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 gmx-users-request at gromacs.org.
>>
>>
>