[AMBER] tleap savepdb command and organic lignads in proteins

From: imtiaz shafiq <imtiazshafiq.gmail.com>
Date: Tue, 30 Mar 2010 18:43:50 +0100

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

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.


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Received on Tue Mar 30 2010 - 11:00:02 PDT
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