AMBER Archive (2009)

Subject: Re: [AMBER] Fwd: Group specification

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 08 2009 - 13:35:43 CDT

you are not using the right syntax for the GROUP lines.
check the manual for details. you are trying to use restraintmask syntax,
which doesn't work there.

On Thu, Oct 8, 2009 at 2:30 PM, Pavan G <pavanamber_at_gmail.com> wrote:

> Hello All,
> I am trying to run a simulation with different restraint weights on
> different groups of atoms in my system. I did find quite a few discussions
> in the forum regarding this issue but none addressed the specific issue of
> selecting certain atoms in a residue. I tried the following without
> success.
> Kindly help me with your comments. If this has already been addressed I
> apologize.
>
> /
> Hold protein tightly
> 10.0
> ATOM :1-654_at_CA,N,C
> END
> Hold ligands
> 5.0
> RES :LG1,LG2,LG3
> END
> Hold lipid tails lightly
> 0.5
> ATOM :LIP_at_C1
> END
> END
>
> Error are mostly on the lines of
> "GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
> GROUP 1 CONSISTS OF ATOMS -
>
> ***PROBLEMS WITH GROUPATOM***** 0 0 0 0 0 0 0
> 0 0 0 0 0 0*******
>
> Number of atoms in this group = 0
> ----- READING GROUP 2; TITLE:
> END
> rfree: End of file on unit 5
>
> "
>
> Thanks,
> Pavan
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