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

[MD]

Thanks Justin.
Ming

On Tue, Jan 2, 2018 at 7:03 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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>
> jalemkul at vt.edu | (540) 231-3129
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>
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