Dear Amber users,
I am trying to use amb2gmx.pl with Ambertools (Amber14). When I used Amber11, I had no problem in this step, however, with Ambertools (Amber14) it complains about rdparm.
amb2gmx.pl --prmtop receptor.top --crd receptor.crd --outname receptor_gmx
| New format PARM file being parsed.
| Version = 1.000 Date = 12/04/14 Time = 12:15:16
WARNING: ATOMIC_NUMBER NOT FOUND IN NEW PRMTOP
Atomic element col.78 left blank in pdb.
You can use Parmed to add atomic_number.
sh: 1: /opt/amber14/bin/rdparm: not found
(...)
Error: pdb and rdparm disagree on number of atoms!
The problem is that rdparm is not found. Surprisingly, when I look for rdparm in /opt/amber14/bin/rdparm, I cannot find it. I have read that in Amber 14 rdparm had been replaced by cppptraj. Is this correct? How could I make amb2gmx.pl work without rdparm?
Thanks a lot for your help in advance!!
Best wishes,
Rebeca.
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
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Received on Sat Jan 10 2015 - 03:00:02 PST
