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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 06 2018 - 05:30:05 PDT
