AMBER Archive (2009)

Subject: Re: [AMBER] Sander and multiple residues

From: Carlos Simmerling (
Date: Thu Apr 09 2009 - 14:21:56 CDT

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 <> 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
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