Topic Options
#14321 - 05/09/07 12:10 PM "bad base passed to useddt"
preeti Offline
Forum Member

Registered: 01/05/05
Posts: 127
Hello,

I am trying to use "GBMV" for modelng water solvent around a protein of 1000 residues or so. Could you please tell me how can i get of the error "bad base passed to useddt" upon use of "nbond" option as below?

thanks, preeti

CHARMM> scalar wmain set 0.0 sele all end
SELRPN> 15681 atoms have been selected out of 15681

CHARMM>

CHARMM> NBOND atom switch cdie vdw vswitch -
CHARMM> ctonnb @ctonnb ctofnb @ctofnb cutnb @cutnb
Parameter: CTONNB -> "14"
Parameter: CTOFNB -> "16.0"
Parameter: CUTNB -> "20"

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB = 20.000 CTEXNB =999.000 CTONNB = 14.000 CTOFNB = 16.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 0 atom pairs and 0 atom exclusions.
There are 0 group pairs and 0 group exclusions.
<MAKINB> with mode 5 found 44562 exclusions and 41362 interactions(1-4)
<MAKGRP> found 13958 group exclusions.
Generating nonbond list with Exclusion mode = 5
VEHEAP> Expanding heap size by 13418496 words.
== PRIMARY == SPACE FOR 13136914 ATOM PAIRS AND 0 GROUP PAIRS

***** LEVEL -4 WARNING FROM <USEDDT> *****
***** BAD BASE PASSED TO USEDDT
******************************************
BOMLEV ( -1) IS REACHED - TERMINATING. WRNLEV IS 5

Top
#14322 - 05/09/07 12:42 PM Re: "bad base passed to useddt" [Re: preeti]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8379
Loc: 39 03 48 N, 77 06 54 W
This is a known problem unrelated to GBMV, but it does depend on the CHARMM release version and how it was compiled. There was a thread on this topic a while ago, probably in the "Bug Reports and Fixes" forum.

It appears that there's a major thread in the "Installation and Performance" forum, and one fix that involves shell (bash or tcsh) setup, esp. on some x86_64 RedHat based systems.

I recall a source code fix as well, which was added to CHARMM, possibly c32b1 or later (I'm exactly not sure).


Edited by rmv (05/09/07 07:35 PM)

Top
#14323 - 05/09/07 07:14 PM Re: "bad base passed to useddt" [Re: rmv]
preeti Offline
Forum Member

Registered: 01/05/05
Posts: 127
Hello,

Now i am able to get rid of the "bad base error" but when it goes through the "dyna" command for GBMV, i get the following error(with regards to "Grid Size"). I do not understand this error at all. Please help.

the input file is like:

set ctofnb = 14.0
calc ctonnb = @ctofnb - 2.0
calc cutnb = @ctofnb + 4.0

scalar wmain set 0.0 sele all end

NBOND atom switch cdie vdw vswitch -
ctonnb @ctonnb ctofnb @ctofnb cutnb @cutnb

GBMV BETA -20 EPSILON 80 DN 1.0 watr 1.4 GEOM -
TOL 1e-8 BUFR 0.5 Mem 10 CUTA 20 HSX1 -0.125 HSX2 0.25 -
ALFRQ 1 EMP 1.5 P4 0.0 P6 8.0 P3 0.70 ONX 1.9 OFFX 2.1 -
WTYP 2 NPHI 38 SHIFT -0.102 SLOPE 0.9085 CORR 1


open read card unit 10 name m0-eq.pdb
read coor pdb unit 10
close unit 10

shake fast bonh tol 1.0e-8 para

open unit 10 write file name "m0-dyna-gbmv.dcd"
OPEN UNIT 21 write card name "m0-dyna-gbmv.rest"

dynamics strt verl nstep 5000 time 0.001 imgfrq 10 iprfrq 200 -
inbfrq 10 nprint 200 ihtfrq 0 ieqfrq 0 ihbfrq 0 iunwri 21 -
iuncrd 10 nsavc 1000 nsavv 0 -
firstt 300.0 finalt 300.0 twindh 1.0 twindl -1.0 -
iasors 1 iasvel 1 ichecw 1 tstruc 300.0 ntrfrq 100 teminc 0 -
atom switch cdie vdw vswitch ctonnb @ctonnb -
ctofnb @ctofnb cutnb @cutnb

close unit 10
close unit 21
______________________________



SHAKE TOLERANCE = 0.10000E-07
NUMBER OF DEGREES OF FREEDOM = 39196

SEED FOR RANDOM NUMBER GENERATOR IS 314159
GAUSSIAN OPTION IS 1
VELOCITIES ASSIGNED AT TEMPERATURE = 300.0000

DETAILS ABOUT CENTRE OF MASS
POSITION : 34.087408 46.857024 27.363632
VELOCITY : 3.76973329E-03 -1.69369150E-03 -8.40302955E-04
ANGULAR MOMENTUM : -6797.1286 -1456.9295 -1798.4101
KINETIC ENERGY : 0.99366924
Readjusting grid size
New Extents: 104 x 104 x 88
Grid size 1903616
Asking for too large a grid change
Exiting.
VCLOSE: Closing unit 10 with status "KEEP"
VCLOSE: Closing unit 21 with status "KEEP"
WARNING: timer state left on: Energy time
WARNING: timer state left on: Nonbond force
WARNING: timer state left on: Gen Born time
$$$$$$ New timer profile $$$$$
Shake Setup 0.07 Other: 0.00
First List 1.51 Other: 0.00
Shake time 0.00 Other: 0.00
dynamc 0.00 Other: 0.00
Dynamics total 0.04 Other: 0.04
INTRNL energy 0.00 Other: 0.00
Energy time 0.00 Other: 0.00
Total time 32.60 Other: 30.97

NORMAL TERMINATION BY DJP
MAXIMUM STACK SPACE USED IS 314184
STACK CURRENTLY IN USE IS 31364
NO WARNINGS WERE ISSUED
HEAP PRINTOUT- HEAP SIZE 10240000
SPACE CURRENTLY IN USE IS 15733366
MAXIMUM SPACE USED IS 180688286
FREE LIST
PRINHP> ADDRESS: 1 LENGTH: 6521840 NEXT: 10002459
PRINHP> ADDRESS: 10002459 LENGTH: 237542 NEXT: 198687649
PRINHP> ADDRESS: 198687649 LENGTH: 3226 NEXT: 198696363
PRINHP> ADDRESS: 198696363 LENGTH: 163896822 NEXT: 362594209
PRINHP> ADDRESS: 362594209 LENGTH: 109363200 NEXT: 471958433
PRINHP> ADDRESS: 471958433 LENGTH: 73007104 NEXT: 544966561
PRINHP> ADDRESS: 544966561 LENGTH: 48758784 NEXT: 593726369
PRINHP> ADDRESS: 593726369 LENGTH: 32604160 NEXT: 626331553
PRINHP> ADDRESS: 626331553 LENGTH: 21823488 NEXT: 648156065
PRINHP> ADDRESS: 648156065 LENGTH: 2196168 NEXT: 650869707
PRINHP> ADDRESS: 650869707 LENGTH: 203868 NEXT: 0

Top

Moderator:  John Legato, lennart