[gmx-users] Adding residue to .rtp file
raji.phy at gmail.com
Thu Oct 18 17:45:49 CEST 2018
I have added the modified residue entry in the rtp file and able to
generate to topology and .gro file. but i got this warning when passing the
pdb2gmx command.What is this about?
"WARNING: there were 74 atoms with zero occupancy and 0 atoms with
occupancy unequal to one (out of 160 atoms). Check your pdb file."
> On 10/5/18 10:23 AM, Raji wrote:
> > Thank you for your reply.
> > "stitching an alkyl group to an existing amino acid should be very
> > straightforward without having to parametrize the entire molecule"
> > Can you please explain me how to do that?
> Functional groups can generally be used like building blocks; they're
> very transferable. You can just amend the residue topology to include
> the new moietie(s), balance charges, and you're largely done. There may
> be some missing bonded terms that have to be parametrized or imported by
> analogy, but it's fairly straightforward. With some basic validation
> (see my many past posts on such topics), you can proceed.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> 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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