AMBER Archive (2003)

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

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Tue Jan 14 2003 - 02:49:55 CST

Hi,
here are some suggestions; I believe top files have to be AMBER-7 style,
have you checked this? Or maybe, your top files haven't been stripped off
waters and counterions? Or otherwise do not correspond to ATOM number ranges
when creating rec and lig parts?

Hope this helps,

  Martin

> 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
> +++++++++++++++++++++++++++++++++++++++++++++
>
>