Re: [AMBER] Error in estrogen-raloxifene tutorial

From: Jason Swails <>
Date: Tue, 1 Jun 2010 09:41:22 -0400


On Tue, Jun 1, 2010 at 5:34 AM, vaibhav dixit <>wrote:

> 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
> error.
> Thanking you all in anticipation and waiting for a reply...
> Error is given below
> -----------------------
> [vaibhav.localhost Estrogen_Raloxifene]$ $AMBERHOME/bin/ -O -i
> -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!

Look at 1err.solvated.prmtop. %FLAG POINTERS is in every single prmtop file
that I have ever seen (I daresay it must be present). This means that
1err.solvated.prmtop is an invalid prmtop file. I just looked at it, and it
appears corrupted for some reason (try to vi the file, it is a binary
file). I have placed 1err.solvated.prmtop on a separate location that you
can download and try:

Try downloading the file from there and using that one instead.

Good luck!

NOTE: All files have been retained for debugging purposes. Type
> --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:
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Jun 01 2010 - 07:00:11 PDT
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