AMBER Archive (2008)

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

From: N.R. Jena (nrjena_at_gmail.com)
Date: Thu Dec 04 2008 - 05:01:36 CST

Thanks Florent Barbault. It seems to me that my definations of LIGRES,
LIGPRI and LIGMAP are okay. I need to know what is the meaning of this
error. This might help me to track its cause.

On Thu, Dec 4, 2008 at 4:32 AM, Barbault Florent
<florent.barbault_at_paris7.jussieu.fr> wrote:
> 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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-- 
Nihar Ranjan Jena
C/O: Prof. Ying-Chieh Sun
Department of Chemistry, National Taiwan Normal University, 88,
TingChow Road, Section 4, Taipei 116, Taiwan
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