AMBER Archive (2004)

Subject: Re: AMBER: mm_pbsa problem

From: david.evans_at_ulsop.ac.uk
Date: Fri Jul 02 2004 - 05:53:23 CDT

Hi,

I had the same issue - a mm_pbsa calculation that worked fine with
GB, and with the alternative PB code Delphi, but crashed (only on
particular frames) with pbsa. Unfortunately I was unable to figure it
out, so am currently just using Delphi.

Dave Evans
London School of Pharmacy

---- Message from steven.j.enoch_at_gsk.com at 2004-07-02 11:29:57 ------
>Dear AMBER users,
>
>I am trying to perform mm_pbsa calculations on snapshots from a
300ps md
>simulation carried out in explicit water with the pbsa module of
AMBER 8 on
>an SGI origin with the following set up:SGI 300 MHZ IP27 processors,
CPU:
>MIPS R12000 Processor Chip Revision 2.3, FPU: MIPS R12010 Floating
point
>chip revision 2.3, OS IRIX 6.5.20M.
>
>The caluclation has no problems with the complex, or the receptor
parts,
>however when its tries to calculate the ligand contributions the
program
>crashes with the following error reported in the pbsa_lig.1.out file:
>
>======== Setting up Grid Parameters ========
>Using bounding box for grid setup
>Bounding Box Center: 35.664 10.838 17.527
>Xmin, Xmax, Xmax-Xmin: 31.182 40.146 8.964
>Ymin, Ymax, Ymax-Ymin: 5.985 15.690 9.705
>Zmin, Zmax, Zmax-Zmin: 11.489 23.565 12.076
>beginning box center at level 1 35.664 10.838 17.527
>beginning box center at level 2 35.664 10.838 17.527
>Grid dimension at level 1 5 7 7
>Grid origin corrected at level 1 23.664 -5.162 1.527
>Grid dimension at level 2 35 35 41
>Grid origin corrected at level 2 26.664 1.838 7.027
>PB Bomb in setgrd(): focusing grid too large 2
>reset fillratio to a larger number 2.000
>
>I have tried running a gbsa simulation at that works fine, so I know
the
>parameter files are OK, interestingly sometimes the pbsa calc runs
for
>several ligand snapshots, with everythng looking fine and then it
stops
>with the same error.
>
>Any help with this would be greatly appreciated - as its starting to
drive
>me crazy!!!
>
>Thanks
>
>Steve
>
>
>Input file
>
>@GENERAL
>#
>PREFIX 1_10
>PATH ./
>#
>COMPLEX 1
>RECEPTOR 1
>LIGAND 1
>#
>COMPT ../md_30ps_avd+btn.top
>RECPT ../md_30ps_avd.top
>LIGPT ../md_30ps_btn.top
>#
>#
>GC 1
>AS 0
>DC 0
>MM 1
>GB 1
>PB 1
>MS 1
>NM 0
>#
>#
>@PB
>#
>PROC 2
>REFE 0
>INDI 1
>EXDI 80.0
>SCALE 2
>LINIT 1000
>PRBRAD 1.6
>RADIOPT 0
>#
>#
>@GB
>#
>IGB 1
>GBSA 1
>SALTCON 0
>EXTDIEL 80.0
>INTDIEL 1.0
>SURFTEN 0.0072
>SURFOFF 0.00
>#
>#
>@MM
>#
>DIELC 1.0
>#
>#
>@MS
>#
>PROBE 0.0
>#
>#
>@NM
>#
>DIELC 4
>MAXCYC 10000
>DRMS 0.0001
>#
>#
>@MAKECRD
>#
>BOX No
>NTOTAL 3460
>NSTART 1
>NSTOP 50
>NFREQ 5
>#
>NUMBER_LIG_GROUPS 1
>LSTART 1918
>LSTOP 1948
>NUMBER_REC_GROUPS 1
>RSTART 1
>RSTOP 1917
>#
>#
>@TRAJECTORY
>#
>TRAJECTORY ../md_300ps.crd
>#
>
>
>
>--------------------------------------------------------------------- 

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