[gmx-users] Convert CNS .top into a GROMACS .itp for a small ligand?

Justin Lemkul jalemkul at vt.edu
Mon Aug 19 16:27:43 CEST 2013

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 force
>> 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 | (410) 706-7441


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