Re: [AMBER] Problem in saving amber prmtop file from DNA pdb file creacted using server ?

From: David A Case <>
Date: Thu, 4 Oct 2018 08:54:50 -0400

On Thu, Oct 04, 2018, Subrata Paul wrote:
> I have created a DNA pdb file using server
> to create a pdb. When I
> try to load this pdb in xleap it shows missing new atom types

It seems likely that the residue or atom names used in your PDB file
don't match the IUPAC/PDB standards. Look at the actual error messages
you get: that will tell you which atoms tleap had trouble recognizing,
and give you ideasof what to fix.

(I'll note that the make-na server is really old; you might consider
using something like instead. Or, you could use the
fd_helix() routine in NAB.)


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Received on Thu Oct 04 2018 - 06:00:05 PDT
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