AMBER Archive (2008)

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

From: Cristina Sisu (csds2_at_cam.ac.uk)
Date: Thu Dec 04 2008 - 05:27:48 CST

Hi Jena,

If you check the /snaphot_lig_all.out / you'll see that
in the first snapshot, (see 1) in the residue 435 (residue number in
column 2) ,the corresponding value in column 3 (the one for
electrostatic contribution - BELE I believe ) might be something like
this: ********** , in other words not a number. Why does something like
this happens I am not sure. To bypass this problem I used to remove that
snapshot from the list of snapshots or just remove the residue from
comparison.

Hope that helps,
Cristina

N.R. Jena wrote:
> 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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