[gmx-users] errors position restraints in a linux cluster

[David]

On Thu, 2004-09-30 at 00:42, gerph at correo.unam.mx wrote:
> Dear David,
> I changed the order of the atoms in the top file as you suggested me, but I did
> get only inverted warnings,
> 
> order changed
> *****************
> Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
> /home/inv/evqz/beta/300
> K/tbeta_em.tpr don't match (Na - OW)
> Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
> /home/inv/evqz/beta/300
> K/tbeta_em.tpr don't match (Na - HW1)
> Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
> /home/inv/evqz/beta/300
> K/tbeta_em.tpr don't match (Na - HW2)
> 
> without changes
> ******************
> Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
> /home/inv/evqz/beta/300K/tbeta_em.tpr don't match (OW - Na)
> Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
> /home/inv/evqz/beta/300K/tbeta_em.tpr don't match (HW1 - Na)
> Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
> /home/inv/evqz/beta/300K/tbeta_em.tpr don't match (HW2 - Na)
> '
Why are you using a tpr file for input? (not that it shouldn't work)
though... Anyway, the order of the atoms still seems to be problematic,
there has to be one-to-one correspondence between coordinates and
topology. Did you change the order in both files by any chance?

> another idea.
> 
> It sounds good your announce about the realese of new version, I will happy to
> upgrade.  
> 
> > On Tue, 2004-09-28 at 22:07, gerph at correo.unam.mx wrote:
> > > Dear all,
> > > 
> > > recently, I get access to a linux-cluster in my university to run
> > gromacs,
> > > however, after a few days of test, with errors, I saw that the
> > administers
> > > installed gromacs 3.1.1. Previusly I did a test with my protein in a
> > single
> > > linux workstation with gromacs 3.2.1 without problems and then I tried
> > run the
> > > same MD steps in the cluster but I am having the next problem with
> > position
> > > restraints and Na,
> > > 
> > > Back Off! I just backed up mdout.mdp to #mdout.mdp#
> > > Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> > > checking input for internal consistency...
> > > WARNING 1 [file /home/inv/evqz/beta/300K/pr.mdp, line unknown]:
> > >   Can not do sorting without shuffling. Sorting turned off.
> > > Excluding 3 bonded neighbours for Protein_E 1
> > > Excluding 1 bonded neighbours for SOL 27509
> > > Excluding 1 bonded neighbours for Na 20
> > > processing coordinates...
> > > Reading file /home/inv/evqz/beta/300K/tbeta_em.tpr, VERSION 3.1.1
> > (single precision)
> > > Reading file /home/inv/evqz/beta/300K/tbeta_em.tpr, VERSION 3.1.1
> > (single precision)
> > > Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
> > > /home/inv/evqz/beta/300K/tbeta_em.tpr don't match (OW - Na)
> > > 
> > > Warning: atom names in /home/inv/evqz/beta/300K/tbeta.top and
> > > /home/inv/evqz/beta/300K/tbeta_em.tpr don't match (HW1 - Na)
> > 
> > This is a serious error, but easy to fix. The order of the atoms in the
> > topology is not the same as in the coordinate file. You probably have
> > ions first in one of the files, and water first in the other. Edit the
> > top file with a text editor.
> > 
> > > 
> > > its look the same for the rest of Na
> > > 
> > > I am using gromacs force field and I add #include "ions.itp" in the
> > top file as
> > > well as I arranged the lines of n ions by solvent before run grompp.
> > > I need upgrade to 3.2.1?
> > > I appreciate any insights about this problem. 
> > 3.2.1 contains quite a few bug fixes, but we will also release 3.3.0
> > *real soon now* so it may be good to wait a couple of days..
> > 
> > > 
> > > Thanks in advance,
> > > 
> > > Gerardo Pérez-Hernández
> > > 
> > > -------------------------------------------------
> > > www.correo.unam.mx
> > > UNAMonos Comunicándonos
> > > 
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the 
> > > www interface or send it to gmx-users-request at gromacs.org.
> > -- 
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > 
> 
> 
> -------------------------------------------------
> www.correo.unam.mx
> UNAMonos Comunicándonos
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++