AMBER Archive (2009)

Subject: RE: [AMBER] database

From: Steve Seibold (
Date: Wed Sep 16 2009 - 11:11:47 CDT

Thanks Prof. Case for your response.

Here is what I have written in my

Source leaprc.ff03
Source leaprc.gaff
Loadamberparams ligand.frcmod
Loadmol2 ligand.mol2
dctp=loadPDB ligand.pdb

The error I get is "20 atoms not is residue templates". However, the naming between the ligand.mol2 and the ligand.pdb file are the same. See attachments. The ligand.mol2 has hydrogens while my pdb file does not, but that's ok right?

What is more, when I make a pdb file (savePDB file output.pdb) of the ligand, with leap after I loaded files using the first four lines in my file, that same pdb file cannot be reloaded back into leap without giving me the same error "20 atoms not is residue templates"

I realize that I needed unique names for atoms in the past, but the prepin files had those unique names in them, while the mol2 does not. I think maybe this is where I am confusing the issue?

Thanks, Steve

-----Original Message-----
From: [] On Behalf Of case
Sent: Wednesday, September 16, 2009 11:26 AM
To: AMBER Mailing List
Subject: Re: [AMBER] database

On Wed, Sep 16, 2009, Steve Seibold wrote:

> I have a mol2 file of a ligand which I have used to generate (using
> parmchk) a ligand.frcmod file. So, I have the ligand.mol2 and
> the ligand.frcmod. I changed the atom names of the ligand in my
> protein/ligand complex pdb file so that the names are equivalent to
> those found in the ligand.mol2 file.
> I am now trying to use the file.mol2 as a prepin file so that when
> I load my protein/ligand complex I can generate topology and inpcrd
> files.

Here is the general tleap scheme:

source leaprc.ff99SB (for example)
source leaprc.gaff (to get the parameters needed for the ligand)
loadAmberParams ligand.frcmod (to get the special parameters for your ligand)
RES = loadMol2 ligand.mol2 (where "RES" is the name of the ligand residue)
complex = loadPdb mycomplex.pdb (where this is the pdb file referred to above)
saveAmberParm complex prmtop inpcrd

Basically, the "loadMol2" command does for mol2 files what the "loadAmberPrep"
file does for prepin files.

...hope this helps...dac

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