[gmx-users] help with my errors (RAHUL SURESH)
drrahulsuresh at gmail.com
Fri Jan 19 13:09:35 CET 2018
On Fri, Jan 19, 2018 at 4:59 PM, banijamali_fs <banijamali_fs at ut.ac.ir>
> > 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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