you must build them together and save from leap as a single system.
you haven't given us enough detail to help more than that- is there a reason
to build separately?
On Thu, Apr 9, 2009 at 2:48 PM, Dan Kaps <dan.kaps.yahoo.com> wrote:
> Hello All,
> I am attempting to run a molecular dynamics simulation in Sander. I have a
> chain of three benzene rings with a water molecule above the center benzene
> ring (residues UNK and AGT). I used leap to get .prmtop and .inpcrd files
> for both residues. Although I'm not sure if this is valid, I combined the
> separate .prmtop and .inpcrd into one .prmtop and one .inpcrd file. When I
> ran sander, it completely ignored the presence of AGT. Does anyone have any
> suggestions?
> Thanks,
> Dan Kaps
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 10 2009 - 01:17:14 PDT
