I am not sure how cpptraj would help. I think it is rather ParmEd that can be used for this purpose. But if you go down this route you may just throw out amb2gmx.pl altogether. It doesn't seem to be maintained anymore.
Alternatively, you could try to use a tool of mine called FEsetup you can find here: http://www.ccpbiosim.ac.uk/flagship#fes . Despite its name and the description on that web page it can also do general simulation setup for various MD engines including Gromacs. As it is currently based on AMBER force fields and tools it also converts a AMBER prmtop to a Gromacs top file (and more, e.g. a full equilibration protocol). If that interests you you can drop me an email off-list to sort things out if necessary.
Cheers,
Hannes.
________________________________________
From: Rebeca García Fandiño [regafan.hotmail.com]
Sent: 10 January 2015 10:47
To: amber.ambermd.org
Subject: [AMBER] problem with rdparm in amb2gmx.pl
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 I have read that in Amber 14 rdparm had been replaced by cppptraj.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 - 04:00:02 PST
