Thanks for your help,
I tryed to use tleap again, The prmtop and inpcrd file are saved, while the
problem is There is no bond connection between carbon atoms in Graphene
sheet, any suggestion to solve this problem?
When I tried to use bondbydistance command in tleap script, The prmtop and
inpcrd file could not saved,
Thank,
haiy
2011/7/17 Jason Swails <jason.swails.gmail.com>
> I don't see any indication that tleap actually failed. There are
> errors/warnings that you may want to look into (did you mean to have a
> non-integral charge?), but the prmtop/inpcrd *should* have been built based
> on the leap.log file you attached, I think (nowhere does it say NOT
> building
> prmtop).
>
> Good luck,
> Jason
>
> On Sun, Jul 17, 2011 at 3:27 AM, hai wei <weihy61.gmail.com> wrote:
>
> > Dear Amber community:
> >
> > I tried to do a MD simulation with a protein on top of Graphene sheet.
> > WHen I use tleap to generate prmtop and inpcrd file just load
> Graphene.pdb.
> > It works fine,
> > when I use tleap to generate prmtop and inpcrd file just load protein.pdb
> > It
> > workd fine,
> > While tleap seems to can not save prmtop and inpcrd file when I put
> > Graphene.pdb and protein.pdb together, Can someone instruct me how to
> solve
> > the problem?
> >
> > I have attached the leap.log file in the attachment file.
> >
> > Thanks ,
> >
> > haiya
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Sun Jul 17 2011 - 15:30:02 PDT
