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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Received on Mon Aug 06 2018 - 06:00:06 PDT
