[gmx-users] query about protein-ligand complex
sangeeta at bic.boseinst.ernet.in
Mon Jul 3 07:17:59 CEST 2006
I could not mail you as our net was down,
you asked me "Is your system
properly minimized? "
My question is how can I understand whether my system is properly minimised?
the run is still going on, I can realize that something is going wrong.
But I can not detect it.The log file is giving the error that the system is
not properly minimised.I am giving you the messege,
"2127 2131 176.6 223178260480.0000 3921810030592.0000 0.1330
2128 2129 176.6 69075034112.0000 1233987043328.0000 0.1000
2128 2130 176.6 69075394560.0000 1233986912256.0000 0.1000
2131 2132 176.5 69056528384.0000 1233902108672.0000 0.1000
2131 2133 176.5 69054996480.0000 1233896734720.0000 0.1000
Constraint error in algorithm Lincs at step 9
t = 0.018 ps: Water molecule starting at atom 13339 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Large VCM(group rest): -168597.92188, 112023.07031, -175543.56250, ekin-cm:
will you please give me some suggestion , so that
I can run the system from the beginning?
On Fri, 30 Jun 2006 14:50:44 +0200, Erik Marklund wrote
> On Fri, 2006-06-30 at 17:52 +0530, sangeeta wrote:
> > Dear all,
> > I am trying to run the dynamics of protein-ligand complex following the
> > tutorial "GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1"
> > . I am running position restricted dynamics of the 91az8.pdb protein as
> > mentioned in the tutorial trp.pdb & drg.pdb)in a Linux server machine, I
> > not understand why it is taking such a long time, the machine is not
> > with any other jobs.I ran it before & I stopped the run at 1200 min,
> > is going for about 215 min, & step6.pdb, step7.pdb etc files are being
> > formed, I can not undersyand whether I am doing any wrong step, why it
> > taking such a long time , I don't know , please help.
> stepX.pdb files are generated when things go wrong, for example when
> forces or other quantities becomes NaN or Inf. The log files should give
> some clues about what is happening to your system.Is your system
> properly minimized? Please provide some more information, otherwise it's
> difficult to help you.
> /Erik Marklund
> > regards
> > sangeeta
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> Erik Marklund, PhD Student, Molecular Biopcysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4537 fax: 46 18 511 755
> erikm at xray.bmc.uu.se
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