AMBER Archive (2003)

Subject: RE: mm_pbsa -- COMPT must be specified (correctly)

From: William Wei (william.wei_at_utoronto.ca)
Date: Mon Jan 13 2003 - 11:32:36 CST

Thank you very much for your attention. As you see, the script had found the
Complex, recept and ligand topological files:

> Found COMPT
> /aspirin/william/CMV/NewModel/Dimer/analysis/mm_pbsa/CMV_Di.top =>
> Found RECPT
> /aspirin/william/CMV/NewModel/Dimer/analysis/mm_pbsa/Di_A.top =>
> Found LIGPT
> /aspirin/william/CMV/NewModel/Dimer/analysis/mm_pbsa/Di_B.top =>

Please help me with this annoying problem. Thanks.

Wiliam

-------------------------
William Wei
Faculty of Pharmacy
19 Russell Street
Toronto, ON. M5S 2S2
Tel: 1-416-946-8469
Fax: 1-416-978-8511
Email: william_at_phm.utoronto.ca
       william.wei_at_utoronto.ca

-----Original Message-----
From: gohlke_at_scripps.edu [mailto:gohlke_at_scripps.edu]
Sent: Monday, January 13, 2003 12:01 PM
To: william.wei_at_utoronto.ca; Amber List
Subject: Re: mm_pbsa -- COMPT must be specified (correctly)

Hi,

the error message means that the parmtop file for the complex does not
exist / is not accessible by the script.

Best regards

Holger

>>>>>

William Wei wrote:
>
> Hi all,
>
> I ran into a mm_pbsa problem while I tried to use GBSA. Here is my
> output:
>
> =>> Init data
> Presuming executables of amber suite to be in
> /aspirin/software/amber7/amber7/exe
>
> =>> Reading input parameters
> Found PREFIX => CMVDi
> Found PATH => ./
> Found COMPLEX => 1
> Found RECEPTOR => 1
> Found LIGAND => 1
> Found COMPT
> /aspirin/william/CMV/NewModel/Dimer/analysis/mm_pbsa/CMV_Di.top =>
> Found RECPT
> /aspirin/william/CMV/NewModel/Dimer/analysis/mm_pbsa/Di_A.top =>
> Found LIGPT
> /aspirin/william/CMV/NewModel/Dimer/analysis/mm_pbsa/Di_B.top =>
> Found GC => 0
> Found AS => 0
> Found DC => 0
> Found MM => 0
> Found GB => 1
> Found PB => 0
> Found MS => 0
> Found NM => 0
> Found BOX => NO
> Found NTOTAL => 73151
> Found NSTART => 1
> Found NSTOP => 100
> Found NFREQ => 1
> Found NUMBER_LIG_GROUPS => 1
> Found LSTART => 3739
> Found LSTOP => 7592
> Found NUMBER_REC_GROUPS => 1
> Found RSTART => 1
> Found RSTOP => 3738
> Found TRAJECTORY => ./CMVDi_CnsP_2_2.5ns_mdcrd
> Found IGB 4 =>
> Found SALTCON 0.00 =>
> Found EXTDIEL 80.0 =>
> Found SURFTEN 0.0072 =>
> Found SURFOFF 0.00 =>
>
> =>> Checking sanity
> Checking GENERAL
> Implicit SAS calc by sander
> COMPT must be specified (correctly)
> -----------------
>
> Any idea with my problem? Thanks a lot.
>
> Have a nice day!
>
> William 

--
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++