AMBER Archive (2009)

Subject: Re: [AMBER] Re: AMBER: ligand parameter

From: Bo Baker (
Date: Sun Jan 11 2009 - 18:20:08 CST

Dear Ross:

Thank you for your suggestion.

My problem here is: I use remote access to amber and I don't have the xleap
in my local PC. Also leaprc.ff99SB is not available for Amber7. Referring
to the antechamber tutorial, I run parmchk to get a frcmod file. From the
frcmod file, there are many places need to be adjusted manually.

I try to work on one of the ligands - FAD only. The structure is checked by
VMD and other programs and looks fine. I then load it to leap. Amber created
three new atoms "N6A, C7M and C8M" and added two missing atoms at CA4 8 and
C5A 10. All these modifications leaded to fail in creating parmfiles. Is
there way that one can manually change the pdb file or prep file to fix
these problems?

I have the pdb file and log file attached.

Thank you very much for your advices


On Thu, Jan 8, 2009 at 3:10 PM, Ross Walker <> wrote:

> Hi Bo,
> > I notice this. But I don't know which amber library to look at? And if
> the
> > atom name in the pdb file can't be found in the library, how could the
> > atom
> > be converted to the amber type? it may need some deep knowloadge on
> > chemistry and the forcefield.
> The simplest way to do this is probably to fire up xleap and source the
> leaprc.ff99SB file. Then you can type edit and a residue name - for example
> edit GLY and it will bring up a graphical window with the residue in - you
> can then select to show the names of the atoms from the menu. Normally most
> pdbs have names that match and it is generally just hydrogens which have
> problems so in those cases it is best to just go through and delete the
> hydrogens. In your case it is some of the backbone atoms as well it looks
> like but only a small number of them so you should just be able to go
> through the pdb and adjust them manually to match what you find by using
> the
> edit window in xleap.
> Another thing you can try is to make a note of which residues have
> problems.
> Cut these out of the pdb and make them pdb's in their own right. Then you
> can load these into leap as individual units and see what leap says. If it
> says it is creating new atoms for certain atoms in the pdb and then adding
> other missing heavy atoms then you can edit that unit and see where the
> added atoms went and how they correspond to the misnames ones - which will
> have a empty square shape representing them. From this you should be able
> to
> figure out if it is simply a mis naming problem.
> Good luck,
> Ross
> /\
> \/
> |\oss Walker
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
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