Dear Amber users,
I'd like to use AmberTools on my Desmond trajectories, so I need to convert the Desmond trajectory to Amber prmtop+mdcrd files.
To get mdcrd, I uploaded my Desmond trajectoy to VMD and saved all the frames as mdcrd by picking the file type as crdbox in VMD.
To get prmtop, I saved only one frame from the desmond trajectory as a pdb file in VMD. I was hoping to generate the prmtop using this pdb with tleap. However, as I load the pdb, tleap adds 2 terminal oxygens (OXT) to each of the chains in my protein-peptide complex.
Is there a way to prevent tleap from adding these OXT atoms to the topology file?
If not, I'm assuming I'll have to edit the topology file manually. In that case, would it work if I decreased the NATOM, MBONA, MTHETA, MPHIA by 1 in the POINTERS FLAG and deleted OXT from ATOM_NAME FLAG? (according to the topology file format described in
http://ambermd.org/formats.html)
Thanks in advance,
Aysegul
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Received on Wed Nov 02 2011 - 16:00:50 PDT
