[AMBER] Fixing pdb files prepared in VMD, minor errors

From: Hunter Brown <bassoongoon.earthlink.net>
Date: Mon, 1 Jul 2013 11:43:13 -0600 (GMT-06:00)

So I had recently e-mailed about a problem I had. Most of the errors were caused by the histidine residue being named 'HSD' instead of 'HIS' (which I changed in the PDB file. This left 72 errors (down from 450ish, not bad).

The 72 errors all say something like: atom CD does not have a type, atom OT1 does not have a type, atom OT2 does not have a type.
The problem atoms were CD, OT1, and OT2.

All of the problem atoms were on the ILE and VAL residues, with the exception of 2 on the CVAL residue (if I am not mistaken, CVAL is not a standard residue name, what should I change the name to?).

I think this should be a relatively easy fix, I just do not know what I need to change in the PDB file at this point.

Help greatly appreciated!

-Hunter Brown

Hunter Brown
Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major

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Received on Mon Jul 01 2013 - 11:00:03 PDT
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