Jones de Andrade wrote:
Hi Prof. David.
Yes, it a self created topology. This one is based on another self
created topology that runs perfectly for cyclohexane. It was adapted to
include the dummy atoms.
I guess there is something wrong in the definition of the dummies in the
topology. But I have no clue where it is. Can you provide me some clue
on this?
no time. but start by adding one dummy at a time run EM and check
whether they end up in the same place.
I'll run a single molecule now.
Thanks a lot in advance,
Sincerally yours,
Jones
On 10/11/07, *David van der Spoel* < [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Jones de Andrade wrote:
> Hi Prof. David.
>
> What details do you mean? Actual topology files are attached.
Anything else?
>
> Thanks a lot in advance!
>
> Sincerally yours,
>
> Jones
>
There is something wrong in the topology, youäll have to debug it
yourself...
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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