[AMBER] Error in estrogen-raloxifene tutorial

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Tue, 1 Jun 2010 15:04:21 +0530

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

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

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
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Received on Tue Jun 01 2010 - 03:00:05 PDT
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