Dear Jason:
I add the connnection records in graphene pdb file as you suggested, It
really works.
Thanks very much.
haiy
2011/7/18 hai wei <weihy61.gmail.com>
> 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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>> > > > 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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>> > 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Jul 18 2011 - 16:00:02 PDT
