Dear,
I usually use GaussView to add hydrogen atoms and get file
of small organic molecules like this.
Save the file as pdb and then you will have to edit your pdb file to put it
in AMBER file format for protéina, for example, specifying the type of atom
correctly and worrying about the position of the columns.
Your mistake with this link so maybe it may be in its initial structure.
then use the following commands, for example:
antechamber -fi pdb -fo mol2 -i MNS_H.pdb -o MNS_pre.mol2 -c bcc -pf and
-nc -1
parmchk2 -i MNS.mol2 -o MNS.frcmod -f mol2
Try generating .mol2 with antechamber and then .frcmod with parmchk2
Best regards
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2017-11-25 5:11 GMT-02:00 mirzo <mirzo.jinr.ru>:
> Lachele Foley писал 25.11.2017 08:37:
> > "For preparing frcmod file, I first used the conversion of Gaussian
> > output
> > into the mol2 file then by the help of parmchk command made frcmod
> > file."'
> >
> > What did you do with this frcmod file? You mention it but don't say
> > how
> > you use it.
> >
> > It really helps if you give full details. For example, Dave had to
> > guess
> > that maybe using shake will help. It would help if you show us the
> > mdin
> > files you are using.
> >
> > And, again, in your example, you built something called GLC and saved
> > something called GLA. So, again, this cannot be what you actually did.
> > It
> > is very important to tell us exactly what you are doing. Please copy
> > and
> > paste the exact commands you used.
> >
> > BTW, there are no hydrogens with zero vdW parms in GLYCAM06j.dat
> > (except
> > the HW for TIP3P, which isn't really glycam). We got rid of such
> > terms
> > because we had observed behavior like what you describe, but not in
> > plain
> > glucose. With our charge sets, it would happen very, very rarely and
> > only
> > in very highly charged situations, for example when a carboxylate group
> > was
> > involved.
> >
> > If you are using charges you made yourself, it is possible that the
> > charges
> > are out of balance for the force field and that they are causing this
> > behavior.
> >
> >
> > On Fri, Nov 24, 2017 at 5:11 PM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >> On Fri, Nov 24, 2017, Aashish Bhatt wrote:
> >> >
> >> > In the 0GA+ROH library,OH-O is not binding in the preparation of
> topology
> >> > and coordinate file. but is getting bound in equilibration.
> >>
> >> This looks a lot like the case one can have when there is no
> >> Lennard-Jones
> >> (vdW) term on a H atom, and it can move arbitrarily close to a nearby
> >> oxygen
> >> atom. You should check the electrostatic energy at the point around
> >> where
> >> the
> >> OH-O distance goes almost to zero: does it become very negative?
> >>
> >> If you have not done so, try turning on SHAKE for hydrogens (ntc=2).
> >> If
> >> the
> >> dagnosis in the above paragraph is correct, that should prevent this
> >> from
> >> happening.
> >>
> >> [I'd like to encourage all Amber users to switch to gaff2, where there
> >> are
> >> no
> >> longer any hydrogens with zero vdW parameters.]
> >>
> >> ...hope this helps....dac
> >>
> >>
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
>
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Received on Sat Nov 25 2017 - 04:30:03 PST
