AMBER Archive (2009)

Subject: Re: [AMBER] Sander and multiple residues

From: Dan Kaps (dan.kaps_at_yahoo.com)
Date: Thu Apr 09 2009 - 15:02:46 CDT

There is no particular reason to build them separately other than the fact that I don't know how. I tried using the function:
VAR = combine { UNK AGT } where VAR would be the combined residue I could build .prmtop and .inpcrd files for. However, This literally combined the residues i.e. the atoms of AGT occupied the same spatial coordinates as those of UNK (one oxygen atoms in AGT has the EXACT same coordinates of a carbon in UNK) in the .inpcrd file. Is there another way to combine them in leap without altering the spacial coordinates?
Dan

________________________________
From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Thursday, April 9, 2009 3:21:56 PM
Subject: Re: [AMBER] Sander and multiple residues

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_at_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
>
>
>
>
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