Re: [AMBER] tleap savepdb command and organic lignads in proteins

From: Jason Swails <>
Date: Tue, 30 Mar 2010 13:45:32 -0400


What does your .lib file look like?

Does it say "MOL" in there?

All the best,

On Tue, Mar 30, 2010 at 1:43 PM, imtiaz shafiq <> wrote:
> Dear All,
> I have a protein with an organic ligand. I have the force field
> parameters (.frcmod) and .lib files for the ligand. I can easily creat
> the prmtop and inpcrd files for this complex. Now my question is when
> I use savepdb command in tleap to save this complex I have noticed
> that the residue name for ligand change to MOL. I have tried with an
> other ligand and found a similar thing that the ligand name change to
> MOL.
> Further analysis of prmtop file also indicated that it also have a MOL
> entry. Please help me how I can keep the original name of the ligand
> when saving a PDB file with savepdb command or I have to manually
> change it every time.
> Regards
> Imtiaz
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Mar 30 2010 - 11:00:03 PDT
Custom Search