AMBER Archive (2008)

Subject: Re: AMBER: Setting GROUP for pmemd

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Nov 28 2008 - 04:12:07 CST

Although pertaining to a parallel (lost) thread, I finally succeeded
to restrain part of the lipid for pmemd. It is a long mdin as full
specification is needed for each atom to restrain. In accordance with
what Bud Dodson suggested, MD with much lipid and 68,000 molecules of
water is definitely faster than with naked system in GB. Both with
pmemd.
francesco

On Thu, Oct 30, 2008 at 8:29 PM, Robert Duke <rduke_at_email.unc.edu> wrote:
> 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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