[gmx-users] (no subject)

lalitha selvam hayagrivar at hotmail.com
Fri May 12 07:50:41 CEST 2006

Dear sir,

    i'm a new user of gromacs.i've done the installation correctly.while
    simulating my protein i encounter some of the problems.please give me ur
    suggetions or any reference to overcome this problem.this is my first
    experience of running the gromacs.kindly look for my problems and answer 
    as soon as possible.Thanks in advance........some of the errors are..

    1..while running  pdb2gmx
        warning :'FE2' not found in residue topology database,trying to use
    'FE'.i know that i've to use PRODGR to construct topology for Fe.but i'm 
    familiar to use it.please tell me the procedure of using it.

    2..when i'm trying to run grompp
        Note: System has non-zero total charge : -6.000002e+00.is it 
    to neutralise the charge, if so genion has to run Na means how much i've 
    add..ie how to calculate it...

    3..with the avialable output file i tried to run mdrun..
       showing the error that can not open File toplo.tpr but my tpr file is
    out3.tpr.i'm giving correctly in command also like mdrun -s out3 -o out4 
    out4 -v..........plz give me ur advice to overcome.
    i'll be helpful if i get the answers..

    thanking you,

Who will win Bollywood’s most coveted IIFA awards? You decide! Cast your 
vote! http://server1.msn.co.in/sp06/IIFA2006/static/weekend.asp

More information about the gromacs.org_gmx-users mailing list