[gmx-users] dihedral not created even with ffbonded.itp all set
jalemkul at vt.edu
Tue Jan 2 13:04:06 CET 2018
On 1/1/18 8:36 AM, MD wrote:
> Hi Gromacs folks,
> I was trying to combine protein with an arbitrary ligand for simulation. I
> think there are two routes to go, one is to create the protein.gro and itp
> with gmx and search the ligand topology on atb or elsewhere, and combine
> them together manually for further simulation. The other is to add topology
> parameters into ffbonded.itp, merged.rtp and use gmx to create the
> ligand.itp file.
> I chose to go with the second route and added the bond, dihedral angles
> parameters into the ffbonded.itp and made sure the names and types are
> consistent in merged.rtp, but the ligand.itp I got from gmx had no
> parameters at all. I had made sure all the names match among pdb,
> merged.itp and ffbonded.itp. Can anyone tell me what could be the problem
Parameter values aren't printed to the topology by pdb2gmx. grompp reads
the list of bonded interactions and looks up the corresponding
parameters from ffbonded.itp.
> Another quick question is regarding the first route, say I went with the
> first route, I will be able to obtain the ligand.itp from atb, but is there
> also a quick way to convert the ligand.pdb to ligand.gro easily? I used atb
> but it only gave back the pdb format back and I will need to manually
> change the sequence of the parameters in a txt file.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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