Dear all,
I am a novice of Amber and wondering if anyone can help me with this
problem. It is a simple task to try to convert a list of Amber restart
files to PDB format files using ptraj command. The OS is Linux (cluster)
and it is Amber version 7. According to the manual the second argument
following ptraj command should be a parameter/topology file. The problem
happened after I specified a topology file:
ptraj
Input the name of an AMBER prmtop or CHARMM PSF: topology_file
Opened file topology_file with mode (r)
Read in control variables
Read in atom names...
ERROR in readParm: ...failed to find CHARGE
But when I opened the topology file, apparently there are charges section in
that file:
%FLAG
CHARGE
%FORMAT(5E16.8)
6.43429413E+00 -6.57825030E-01 -7.50940983E+00 1.82223000E+00
1.82223000E+00
1.82223000E+00 -7.50940983E+00 1.82223000E+00 1.82223000E+00
1.82223000E+00
1.08841798E+01 -1.03484442E+01 -4.64304204E+00 3.49868160E-01
7.12491930E-01
7.12491930E-01 3.44401470E-01 3.88134990E-01 3.88134990E-01 -
1.27556100E-01
-----------
I am really confused and don't know how to solve the problem. Can anyone
help. Any input will be greatly appreciated.
-Fine
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Apr 02 2006 - 06:10:16 PDT
