AMBER Archive (2008)

Subject: Re: AMBER: Setting GROUP for pmemd

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Oct 30 2008 - 14:29:27 CDT

Send the actual mdin files, along with a description of which did and did
not work with pmemd vs. sander.MPI. I noted a caps error below in something
that supposedly worked ("EnD" keyword). Just glancing at the code, I do
believe the keywords are going to be case-sensitive.
Regards - Bob Duke
----- Original Message -----
From: "Francesco Pietra" <chiendarret_at_gmail.com>
To: "Amber" <amber_at_scripps.edu>
Sent: Thursday, October 30, 2008 3:10 PM
Subject: AMBER: Setting GROUP for pmemd

> The pdb is
> RES 1 78 lipid POPC
>
> RES 79 340 protein with capping groups (included in numbering)
>
> RES 341 ligand
> ====
>
> Input for pmemd to restrain protein ligand and POPC (the other residues
> are WAT)
>
> /
> Keep ...
> 32.0
> RES 1 341
> END
> EnD
>
> worked fine.
> =========
>
> The I moved to sander.MPI in order to be able to restrain protein,
> ligand and a part only of lipid. Now back to pmemd to restrain protein
> and ligand only
>
>
> /
> Keep ..
> 32.0
> RES 79 341
> END
> END
>
> the out file:
> LOADING THE CONSTRAINED ATOMS AS GROUPS
> 5. REFERENCE ATOM AND COORDINATES
> READING GROUP 1;TITLE:
> GROUP 1 HAS HARMONIC CONSTRAINTS 32.00000
> GRP 1 RES 79 TO 341
> number of atoms ...
> READING GROUP 2; TITLE:
> END
> GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000
> rfree: End of file on unit 5
> ====================
>
> Thanks a lot for pointing out my mistake.
>
> francesco pietra
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