Does your graphene PDB file not have CONECT records? You may have to bond
individual atoms, or (in case a bond was created via bondbydistance that
wasn't intended) remove the unintended bonds created during bondbydistance.
Without the actual leap log file, I can't help any more.
HTH,
Jason
On Sun, Jul 17, 2011 at 6:00 PM, hai wei <weihy61.gmail.com> wrote:
> 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
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> > >
> > >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Jul 17 2011 - 15:30:03 PDT
