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

Justin Lemkul jalemkul at vt.edu
Fri Jan 19 13:51:06 CET 2018

On 1/19/18 7:09 AM, RAHUL SURESH wrote:
> 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

No sane species can have a fractional total charge. Is it possible for a 
molecule to have part of an electron? Of course not. Any topology that 
sums to a non-integer charge is flawed and needs to be corrected.


>>> 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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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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