I am extremely sorry for the late reply. It was an error about mismatch
atom name.
I have changed each and every atom name according to .lib file using Pymol
and it solved my problem.
If there are other ways to change atom names please suggest and I could not
find match_atomname program in Amber16.
Thank you very much for your instant replies.
:)
On Mon, Aug 6, 2018 at 6:27 PM Junmei Wang <junmwang.gmail.com> wrote:
> You may try to use match_atomname program in antechamber package to solve
> the atom name mismatch problem.
>
> Junmei
>
>
>
> On Mon, Aug 6, 2018 at 8:04 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Mon, Aug 06, 2018, Anuja Ware wrote:
> >
> > > I am new to AMBER. I was trying to generate a .lib file (parameters)
> for
> > a
> > > non-standard residue, ubiquinone. I have downloaded crystal
> > > structure pdb of it. I have optimized it adding H (with gaussian),
> > derived
> > > RESP charges and then generated .prepi and .frcmod files using
> > > antechamber. I have also generated a .lib file of optimized structure.
> > My
> > > problem is that whenever I load .lib file, tleap generates .prmtop and
> > > .inpcrd files for the pdb which is optimized with Gaussian. But
> > whenever I
> > > tried to load the crystal structure pdb the .lib file parameters are
> not
> > > matching with it and it gives errors and warnings. Can u just suggest
> > > where I m going wrong?
> >
> > There is probably some naming mismatch between the crystal PDB and the
> > .lib file, but that is just a guess. Just a report saying that "it
> > [tleap?] gives errors and warnings" does not give enough information to
> > allow others to help. Can you give more details, including the *exact*
> > error messages you are getting? And check to see that the residue and
> > atom names in the .lib file match those in the PDB file.
> >
> > ....dac
> >
> >
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> >
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Received on Mon Sep 03 2018 - 04:30:01 PDT
