AMBER Archive (2003)

Subject: Re: saveAmberParm problems in xleap

From: Wayne Dawson (dawson_at_nih.go.jp)
Date: Thu May 08 2003 - 04:02:45 CDT

Just to follow up....
David Case wrote in regard to my leap.log file:

> You have *lots* of errors when you load your pdb file. It may in
> fact be that LEaP gets confused with all of the "remove" commands,
> and/or that some of these commands are not really correct.
>
> What you should do is edit the input pdb file to make things
> correct: get the residues you want in there, either remove hydrogens
> or use protonate to re-name them to IUPAC standards, etc.

It seems you were right.

With Insight generated PDB files: For EACH residue, the hydrogens are
placed at the end of the list of atoms (before the next N). So I found
it easiest to simply remove them. You also have to remove the "cap"
(OH) at the C terminus. As someone else suggested, it should be loaded
it using "loadPdbUsingSeq"

> PrtnSeq = { NXXX1 ... ... CXXXn }
> Prtn = loadPdbUsingSeq Prtn.pdf PrtnSeq

The InsightII default for HIS is HIE it seems. I was able to get it
through that step without any problems after I modified the PDB file.

regards,
Wayne