AMBER Archive (2000)

Subject: Re: Problems using IBELLY in AMBER6

From: Marios Philippopoulos (mphilip_at_sickkids.on.ca)
Date: Tue Feb 29 2000 - 09:43:04 CST

Sorry, my omission. I had indeed included two END statements at the end of the
input file. It was like this:

--------------------INSERT-------------------------------
..........
Allow only solvent (residues 3 to 824) to move:
 RES 3 824
 END
END

----------------END---INSERT------------------------------

I still got the same output:

--------------------INSERT--------------------------------

......................

Warning: Although EWALD will work with belly
(for equilibration), it is not strictly correct!

    LOADING THE BELLY ATOMS AS GROUPS

    ----- READING GROUP 1; TITLE:
 Allow only solvent (residues 3 to 824) to move:
 GRP 1 RES 3 TO 824
      Number of atoms in this group = 2466
    ----- READING GROUP 2; TITLE:
 END

     rfree: End of file on unit 5

--------------------END---INSERT--------------------------

Thanks,
Marios

Bill Ross wrote:

> I was using BELLY in an effort to minimize and equilibrate the solvent
> prior to doing so on the full system.
>
> I'm of the opinion that belly isn't needed at the minimization
> stage when solvent is placed by 'normal' means, i.e. no major
> vdw overlaps, as is the case with leap's solvent placement.
>
> However, belly can be quite useful in the eqilibration stage,
> depnding on one's equilibration strategy (see the discussions
> of this in the Questions section on the amber web).
>
> And in any case, one needs to be able to specify a belly..
>
> The problem is that ewald is turned on by default
>
> Sorry, I had forgotten that this is the case in mber6.
>
> &end
> Allow only solvent (residues 3 to 824) to move:
> RES 3 824
> END
>
> The END you have ends the first (and in this case only)
> belly 'section' specification -- another END is called for
> to end the belly group specification itself.
>
> Maybe we should change the keywords to ENDSECTION and
> ENDGROUP to make this clearer. ('section' here is my own
> word for the 'group within a GROUP'.)
>
> See the Appendix on group definition.
>
> Bill Ross 

--
Marios Philippopoulos, PhD
Structural Biology and Biochemistry Programme
Hospital for Sick Children
555 University Avenue
Toronto Ontario Canada M5G 1X8

mphilip_at_sickkids.on.ca