I've attached the log file. There's nothing special about the input coordinates really. Its just three benzene rings in a chain. The center benzene ring has two of the carbons replaced by oxygens. Above the center benzene ring is a water molecule (the distance is approximately equal to the height of the benzene ring although this is not essential). And yes, I am loading the coordinates from a .pdb which is why I can't understand why the combine function does not preserve the coordinates...
Thanks,
Dan
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, April 9, 2009 4:05:23 PM
Subject: Re: [AMBER] Sander and multiple residues
are you loading the coordinates from a pdb? i have never had trouble loading
a system with multiple molecules so I guess I can't understand the problem,
try to say exactly what you are doing. maybe include your leap script and a
description of the special input coordinates?
On Thu, Apr 9, 2009 at 4:02 PM, Dan Kaps <dan.kaps.yahoo.com> wrote:
> 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.gmail.com>
> To: AMBER Mailing List <amber.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.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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> >
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- application/octet-stream attachment: leap.log
Received on Sun Apr 12 2009 - 01:08:10 PDT
