I was wondering if anyone got support for amber topology and
trajectory formats working in CVS pymol. Here is what I tried:
1. I tried to build PyMOL using "Approach 2" (i.e. standalone PyMOL
using Makefile) in RedHat7.3 (python1.5, gcc-2.96). The build
finishes successfuly (i.e. no error just bunch of warnings) but when
I try to run 'pymol.com', the following error appears:
Traceback (innermost last):
File "/usr/local/pymol/modules/pymol/__init__.py", line 92, in ?
import pymol
File "/usr/local/pymol/modules/pymol/__init__.py", line 220, in ?
import cmd
File "/usr/local/pymol/modules/pymol/cmd.py", line 752, in ?
from importing import \
File "/usr/local/pymol/modules/pymol/importing.py", line 26, in ?
from pymol import m4x
File "/usr/local/pymol/modules/pymol/m4x.py", line 17
from chempy import cex as CEX
^
SyntaxError: invalid syntax
2. I repeated the same build procedure but in RedHat8.0 (python2.2,
gcc-3.2) and, to my big surprise, it builds and runs! (I find it hard
to believe that a switch from python1.5 to python2.2 would be that
easy, but I'd surely not complain as RH8.0 is my current working OS).
In any case, I tried to load amber topology and trajectory:
load test.top
(this seems to succeed as the message appears:
ObjectMolecule: Assuming this is an Amber6 topology file.
Executive: object "test" created.)
load_traj test.trj
..and here is where I got stuck, the message is:
CmdLoadTraj-Error: must load object topology before loading trajectory!
Was someone successful to get this working?
Thanks very much,
-Viktor
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Viktor Hornak
SUNY at Stony Brook
Stony Brook, NY 11794-5115 E-mail: Vik...@su...
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