Hi,
On Fri, Oct 13, 2017 at 1:10 PM, Eiros Zamora, Juan
<j.eiros-zamora14.imperial.ac.uk> wrote:
>
> Does anyone have a suggestion on how can I convert the atom names in NAMD to AMBER? I’ve found a couple of online tools (http://feig.bch.msu.edu/mmtsb/Convpdb.pl and http://thegrantlab.org/bio3d/html/convert.pdb.html ) but neither change the problematic atom names.
You could try using the new 'change' command in the GitHub version of
cpptraj to change the atom names (this is what I do when converting
CHARMM pdbs to Amber). You do need to know what atom names need to be
converted. You can figure this out by loading the forcefield into leap
and using the 'desc' command to see what the Amber templates expect
(e.g. 'desc NASP.1' to see the atom names in NASP residues, etc). So
for example:
parm namd.pdb
trajin namd.pdb
change atomname from :ASP.CAY to CA
change atomname from :ASP.CY to C
...
trajout amber.pdb
I'm guessing at the mapping from NAMD, but you get the idea. Hope this helps,
-Dan
PS - You could also try the 'atommap' command, probably with the
'byres' keyword, but I've only extensively tested that on small
molecules.
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Oct 13 2017 - 11:00:02 PDT
