[gmx-users] OPLS-AA with TIP4P water, error during energy minimization

[David]

On Wed, 2004-05-05 at 05:30, Sunita Patel wrote:
> Dear gmx_users,
> 
> I am trying to simulate a protein with explicit TIP4P water by using

> Even with this warning message I proceed with editconf and genbox. There
> is no warning during this steps. But while performing grompp for energy
> minimization I got following fetal error
> 
> 
> ===========================   grompp ====================================
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 243951 of the 243951 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 243951 of the 243951 1-4 parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> Excluding 2 bonded neighbours for SOL 60
> Excluding 2 bonded neighbours for SOL 7088
> WARNING 1 [file "4pti.top", line 8422]:
>   System has non-zero total charge: 6.000000e+00
> 
> processing coordinates...
> Fatal error: number of coordinates in coordinate file (solvation.gro,
> 29724)
>              does not match topology (4pti.top, 29484)
> 

the difference is 240 atoms, 60 tip4p. They are either missing from the
topology or double in the gro file.

> ====================================================================
> 
> So what could be the reason for this error.
> Thank for any suggestion.
> 
> regards,
> Sunita
> -------------------------------------------------------------------------------
> Sunita Patel
> Biophysical Lab.,
> Dept. of Chemistry,
> Indian Institute of Technology(IIT) Bombay,
> Powai, Mumbai, Maharashtra,
> INDIA-400076.
> 
> Tel: (91)-22-25764176.
> Email:sunita at chem.iitb.ac.in
> -------------------------------------------------------------------------------
> 
> 
> 
> _______________________________________________
> 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++