Dear Amber community members,
I'm interested to calculate binding free energies for some of my ligands. In
this regard I'm trying to use the following python script based tutorial
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm
After copying the Est_Rec_top_mdcrd.tgz and extracting it to get the
necessary file, I ran the script using the command given in the tutorial.
But I'm getting the following error and only two files are generated namely:
_MMPBSA_gb.mdin and _MMPBSA_pb.mdin
Please find time and see if you could help me in tracing the source of the
error.
Thanking you all in anticipation and waiting for a reply...
Error is given below
-----------------------
[vaibhav.localhost Estrogen_Raloxifene]$ $AMBERHOME/bin/MMPBSA.py -O -i
mmpbsa_2b.in -o FINAL_RESULTS_MMPBSA.dat -sp 1err.solvated.prmtop -cp
complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd
ptraj found! Using /home/vaibhav/software/amber10/exe/ptraj
sander found! Using /home/vaibhav/software/amber10/exe/sander (serial only!)
Assuming /home/vaibhav/software/amber10/exe/sander is part of
amber9 or amber10. Using old PB input file.
Error: Could not find %FLAG POINTERS in topology file 1err.solvated.prmtop!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
------------------------------------------------------
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Tue Jun 01 2010 - 03:00:05 PDT
