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

[gerph at correo.unam.mx]

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)

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