[gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?
devicerandom at gmail.com
Mon Aug 19 16:44:21 CEST 2013
Okay, clearer now. Will see what I can do. Thanks a lot for your help.
2013/8/19 Justin Lemkul <jalemkul at vt.edu>
> On 8/19/13 10:22 AM, massimo sandal wrote:
>> 2013/8/19 Justin Lemkul <jalemkul at vt.edu>
>>>> An .itp is just a topology, so it's identical to a .top except that it
>>> does not have system-level directives and does not #include a parent
>>> field. Manual sections 5.7.1 and 5.7.2 describe the relevant contents.
>>> I know - just to be sure we're understanding each other, I know it's
>> identical to a *GROMACS* .top , not the CNS one. :)
>> In 5.7.1 and 5.7.2 yes,there is description of the topology file format,
>> but I'm unsure what you precisely meant with the ffbonded.itp / charge
>> groups stuff you said I have to refer in.
> Run something through pdb2gmx with Gromos96 and you will see what I mean.
> For instance, in [bonds] each atom pair must have a gb_* term that
> corresponds to the bonded parameters. Unlike OPLS, AMBER, etc. the bonded
> parameters are not simply looked up when using Gromos96. Therefore, you
> have to match your atom types to their numbers, then look up the
> appropriate gb_*, ga_*, gd_*, and gi_* entries from ffbonded.itp. In the
> CNS .top files I was looking at, there are no charge groups. You will need
> to find a way to assign them. Gromos96 uses charge groups to break down
> chemical functional groups.
> Justin A. Lemkul, Ph.D.
> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
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