AMBER Archive (2008)

Subject: Re: AMBER: MM/GBSA Error during deccomposition

From: Barbault Florent (florent.barbault_at_paris7.jussieu.fr)
Date: Wed Dec 03 2008 - 14:32:14 CST

Hello

I already had this. For myself, this problem has arose from a bad
definition of LIGRES, LIGPRI and LIGMAP. However, I still didn't
understand what was the meaning of "missing BELE...". So my suggestion
is to have a look on the ligand definition... Hope this will help you.

Regards
Florent Barbault

On Wed, 3 Dec 2008 20:01:04 +0800
  "N.R. Jena" <nrjena_at_gmail.com> wrote:
> Dear Amber users,
>
> I got an error like "Missing BELE for MM in 1 (residue 435)" while
> decomposition of complex. Residue 435
> corresponds to one of the water molecules of the water box. I
>followed
> the previous question-answer section in this regard, but could not
> find any answer. my input file is like this:
>
> @GENERAL
> PREFIX snapshot
> PATH ./snapshot/
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./complex4_min_Ions.top
> RECPT ./1q3d_H.top
> LIGPT ./H894_H.top
> GC 0
> AS 0
> DC 1
> MM 1
> GB 1
> PB 0
> MS 0
> NM 0
> @PB
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80
> SCALE 2
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0
> RADIOPT 0
> NPOPT 1
> CAVITY_SURFTEN 0.0072
> CAVITY_OFFSET 0.00
> SURFTEN 0.0072
> SURFOFF 0.00
> CUTRES 12
>FILLRATIO 2
> @MM
> DIELC 1.0
> @GB
> IGB 1
> GBSA 2
> SALTCON 0.00
> EXTDIEL 80
> INTDIEL 1.0
> SURFTEN 0.0072
> SURFOFF 0.00
> @MS
> PROBE 0.0
> @DECOMP
> DCTYPE 2
> COMREC 1-5474
> COMLIG 5475-5521
> COMPRI 1-5521
> RECRES 1-5474
> RECPRI 1-5474
> RECMAP 1-5474
> LIGRES 1-47
> LIGPRI 1-47
> LIGMAP 5475-5521
>
> It will be quite helpful, if someone will guide me.
>
> With warm regards,
>
> (N.R. Jena)
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