AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jan 07 2009 - 22:10:20 CST

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:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber