AMBER Archive (2003)

Subject: Re: question about mm_pbsa

From: Joachim Reichelt (Reichelt_at_gbf.de)
Date: Mon Mar 10 2003 - 06:43:58 CST

Couse I want too use it too and got the same using the
.../Examples/05_MMPBSA_Decomp_Residue/

So my question is: which version of DELPHI shoud I use?
Is there an alternative e.q. APBS?
(DELPHI is now 250 US-$, APBS is free)

Holger Gohlke schrieb am 03/10/2003 04:31 AM:

>Hi,
>
>in the current form, the parser for the decomposition information needs
>ranges in the form "x-y", where x and y are residue numbers. So for your
>input on the COMLIG, COMPRI, ... lines below, you need to give "1-1"
>instead just "1".
>
>Best regards
>
>Holger
>
>
>
>>Hi:
>> I run MD for my ligand with H2O. I want to decompose the interaction enery
>>between the ligand and H2O. First, I generated the snapshots file from the
>>trajectory. It works fine. Then I tried to decompose the energy, my input file
>>is like:
>> PREFIX dhnp-dc
>>PATH ./
>>COMPLEX 1
>>RECEPTOR 1
>>LIGAND 1
>>#
>>COMPT ./dhnp.prmtop
>>RECPT ./dhnp-wat.prmtop
>>LIGPT ./dhnp-now.prmtop
>>#
>>GC 0
>>AS 0
>>DC 1
>>#
>>MM 1
>>GB 1
>>PB 0
>>MS 0
>>#
>>NM 0
>>#
>>DCTYPE 2
>>#
>>COMREC 2-1218
>>COMLIG 1
>>COMPRI 1
>>RECRES 1-1217
>>RECPRI 1
>>RECMAP 2-1218
>>LIGRES 1
>>LIGPRI 1
>>LIGMAP 1
>>
>>And when I run it, I always get:
>>=>> Init data
>> Presuming executables of amber suite to be in /usr/local/amber7/exe
>>
>>=>> Reading input parameters
>> Found PREFIX => dhnp-dc
>> Found PATH => ./
>> Found COMPLEX => 1
>> Found RECEPTOR => 1
>> Found LIGAND => 1
>> Found COMPT => ./dhnp.prmtop
>> Found RECPT => ./dhnp-wat.prmtop
>> Found LIGPT => ./dhnp-now.prmtop
>> Found GC => 0
>> Found AS => 0
>> Found DC => 1
>> Found MM => 1
>> Found GB => 1
>> Found PB => 0
>> Found MS => 0
>> Found NM => 0
>> Found DCTYPE => 2
>> Found COMREC => 2-1218
>> Found COMLIG => 1
>> Found COMPRI => 1
>> Found RECRES => 1-1217
>> Found RECPRI => 1
>> Found RECMAP => 2-1218
>> Found LIGRES => 1
>> Found LIGPRI => 1
>> Found LIGMAP => 1
>> Found DELPHI => /home/gohlke/src/delphi.98/exe.R10000/delphi
>>
>>=>> Checking sanity
>> Checking GENERAL
>> Implicit SAS calc by sander
>> Checking DC
>> Wrong format for decomp: 1
>> But I don't know what's wrong? Anybody can help me?
>>
>>Thanks.
>>
>>Lishan
>>
>>
>
>
> 

-- 
Mit freundlichen Gruessen                         Best Regards

         Joachim Reichelt

			SB  - Strukturbiologie
              GBF - Gesellschaft fuer Biotechnologische Forschung
                    German Research Centre for Biotechnology

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