On Tue, Mar 12, 2013 at 9:09 AM, tianchuan881 <tianchuan881.hotmail.com>wrote:
> Hi amber,
> I prepared my CYP system , andI removed the heme. To my surprise, in
> tleap-saved pdb the ligand is broken as well(the tleap saved pdb which has
> heme the ligand is broken) Thus, I doubt the problem is in the frcmod file.
> While in my process, the frcmod file is generated by amber. Could you give
> me some hints on how to modify frcmod file?
> By the way, in your system, is the ligand docked into the protein or not?
> The frcmod file is attached.
> best regards
> tianchuan
>
Perhaps my last email was confusing. Just because bonds do not appear in a
ligand PDB file written by tleap does NOT mean that the bonds are not added
to the topology file.
Visualize the prmtop and the inpcrd file directly (do NOT draw conclusions
from a tleap-generated PDB -- it does not store CONECT records). If the
prmtop/inpcrd combo appears to have missing bonds, THEN you have a problem.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Mar 12 2013 - 14:00:03 PDT
