Hi all,
Recently I use CHAMBER program transformed CHARMM parameter file to
AMBER prmtop file and run a replica exchanging self-guided (RXSG) MD. I
met the problem when I use ptraj to extract the RXSG MD trajectory. The
error information was shown as follows:
WARNING in scanDouble: ...scanning chrg
Residue labels:
TYR TYR ASP PRO GLU THR GLY THR TRP TYR
SOD SOD WAT WAT WAT WAT WAT WAT WAT WAT
WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
...
WAT WAT WAT WAT WAT
There were errors upon reading parm file!!!
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin ../step5/crd/rxsg25.mdcrd.001 rxsgldtraj rxsgldid 1
Checking coordinates: ../step5/crd/rxsg25.mdcrd.001
It seems that ptraj can't recognize my parm file. So I also update
Amber12 to do some patching, but still have the same problem. I know
that the parm file from CHARMM force field using CHAMBER may have some
differences from AMBER parm on format like %FLAG CHARGE：
charmm to amber parm file:
%FORMAT(3e24.16)
-0.5466849549786422E+01 0.6013534504765064E+01
0.6013534504765064E+01
0.6013534504765064E+01 0.3826794684850495E+01
0.1822283183262141E+01
-0.3280109729871853E+01 0.1640054864935927E+01
0.1640054864935927E+01
but amber parm file:
%FLAG CHARGE
%FORMAT(5E16.8)
3.36930327E+00 3.45859254E+00 3.45859254E+00 3.45859254E+00
1.03320441E+00
1.42498386E+00 4.73050908E+00 4.97468790E-01 4.97468790E-01
-1.22344522E+01
and charmm to amber file seems to have no %FLAG BOX_DIMENSIONS
information in parm file. But I have already run the simulation using
this parm file successfully. So I think this parm file is ok.
I have no idea about this error. I wonder how to solve the problem
and why ptraj can't read my parm file?
Hope for your reply! Thanks a lot~
Wei Liu
--------------------------------------
Institute of Theoretical and Computational Science
East China Normal University
ShangHai，china，200062
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Received on Tue Sep 02 2014 - 06:30:02 PDT
