Hi,
Perhaps you should pay attention to the residue names of non-standard residues and unify them in the ligand file and complex file. Then, when you use tleap to generate .lib file, you should use the same name while you load the mol2 file of the ligand into tleap.
Hope this helps...if not, give us more details:)
Kind regards,
Zhonghua
> On 6. Aug 2018, at 11:49, Anuja Ware <ware.anuja.p.gmail.com> wrote:
>
> Dear AMBER users,
> 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?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/pkcs7-signature attachment: smime.p7s
Received on Mon Aug 06 2018 - 05:00:01 PDT
