[gmx-users] help with my errors (RAHUL SURESH)

[RAHUL SURESH]

On Fri, Jan 19, 2018 at 4:59 PM, banijamali_fs <banijamali_fs at ut.ac.ir>
wrote:

> > Hi there,
> >
> > 1. I'm working on MOF (metal organic framewoks) structures. I'd like to
> > know that if in our topology file we get a decimal figure for the qtot,
> > in which step we made a mistake? and how we can rectify this?
>

qtot defines the charge and that can be neutralized in the genion step. I
am not sure if it works different for MOF

> >
> > 2.  Another question that I have is that when I want to run this
> > command, gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr, I
> > get this error,Too many warnings (1), gmx terminated, I don't now how to
> > rectify this error.
> >
> > I would be very thankful if anyone could help me.
> >
> > these are the warning that I mentioned above:
> > Warning: atom name 57 in topol.top and solv.gro does not match (CU - CU2)
> > Warning: atom name 58 in topol.top and solv.gro does not match (CU - CU2)
> >
> > WARNING 1 [file topol.top, line 114]:
> > 2 non-matching atom names
> > atom names from topol.top will be used
> > atom names from solv.gro will be ignored
>

You can change the name  as in top. so the 2nd error can be eliminated.

> >
> > Fatemeh.
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*