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

From: Hunter Brown <>
Date: Tue, 2 Jul 2013 09:50:46 -0600 (GMT-06:00)

Thanks for your help.

I changed the OT1s to Os which fixed that problem. However after changing OT2 to OXT I am still running into trouble:

FATAL: Atom .R<VAL 40>.A<OXT 17> does not have a type.

All of the problems are with the OXTs on VAL and the CDs on ILE (which I am going to change to CD1, should fix that problem).


-----Original Message-----
>From: David A Case <>
>Sent: Jul 1, 2013 7:44 PM
>To: Hunter Brown <>, AMBER Mailing List <>
>Subject: Re: [AMBER] Fixing pdb files prepared in VMD, minor errors
>On Mon, Jul 01, 2013, Hunter Brown wrote:
>> 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?).
>Just compare the atom names in the PDB file you got from VMD (or wherever)
>versus those in a "real" PDB file that you download from
>CHARMM has used the wrong name for the c-delta of ILE since the beginning
>of time, and also uses OT1,OT2 instead of O,OXT for the terminal
>carboxylate group at the end of the chain.
>CVAL just means: C-terminal valine. Change this to VAL (although I'm a little
>surprised that CVAL didn't work.)
>Another approach is to ask people on the CHARMM or VMD support sites what
>tools they use to create PDB files with correct atom and residue names.
>AMBER mailing list

Hunter Brown
Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major

AMBER mailing list
Received on Tue Jul 02 2013 - 09:00:04 PDT
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