Dear *Jason:
Maybe put the connection records in my Graphene pdb file is a good idea. Any
suggestion how to add connection records to pdb file since so many
connection need to add?
Thanks.
haiy*
2011/7/18 Jason Swails <jason.swails.gmail.com>
> 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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> > > >
> > > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
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> > > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Jul 17 2011 - 18:00:02 PDT
