Dear Amber community members,
Thanks Jason for a prompt help with the tutorial. I could use the new file
successfully.
I'm now trying the same tutorial procedure on my target protein and ligand.
Here I'm getting a different kind of error which is given below. I could not
understand what it exactly means and how could I fix it.
Please find time and see if you could help me with same.
The error is as follows:
---------------
[vaibhav.localhost MMPBSA]$ $AMBERHOME/bin/MMPBSA.py -O -i
mmpbsa_2b.inFINAL_RESULTS_MMPBSA.dat -sp 2PRG_rosi_solvated.prmtop -cp
2PRG_rosi_NW.prmtop -rp 2PRG_nolig.prmtop -lp rosi.prmtop -y *.mdcrd
ptraj found! Using /home/vaibhav/software/amber10/exe/ptraj
sander found! Using /home/vaibhav/software/amber10/exe/sander (serial only!)
Assuming /home/vaibhav/software/amber10/exe/sander is part of
amber9 or amber10. Using old PB input file.
Error: Could not predict mask from topology files! Make sure ligand residues
are
sequential or specify receptor_mask and ligand_mask in the input file.
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
[vaibhav.localhost MMPBSA]$ pwd
/home/vaibhav/vaibhav/amber/2PRG/rosi/MMPBSA
[vaibhav.localhost MMPBSA]$
-------------------------------------------
On 6/1/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> Hello,
>
> On Tue, Jun 1, 2010 at 5:34 AM, vaibhav dixit <vaibhavadixit.gmail.com
> >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
> > 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!
> >
>
>
> 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:
>
> http://crunch.qtp.ufl.edu/~swails/Files/1err.solvated.prmtop
>
> Try downloading the file from there and using that one instead.
>
> Good luck!
> Jason
>
>
> 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
>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 08:00:04 PDT
