[gmx-users] dihedral not created even with ffbonded.itp all set

[Justin Lemkul]

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
> here?

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.

Use editconf.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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