Hi CHARMM users,

I while runing an analisys script for rmsd-rgyr-trajectory correl. I had the following problem:

Please help me to find below the problematic part of the input file and below this the CHARMM output.

Thanks for your help


input
* Compute RMSD and Rg for a MD trajectory: using CORREL tools
*

!Read topology and parameter (aka force field)
read rtf card name /home/lherrera/proyectos/namd/top_all22_prot_cmap_cu.rtf
read para card name /home/lherrera/proyectos/namd/par_all22_prot_cmap_cu.prm

!Read PSF and initial/reference coordinates
read psf card name /home/lherrera/proyectos/charmm/charmm-analysis/files/3gb1_solv.psf
read coor pdb resid name /home/lherrera/proyectos/charmm/charmm-analysis/files/3gb1_solv.pdb
coor copy comp

!Open file unit for trajectory
open read unit 13 file name /home/lherrera/proyectos/charmm/charmm-analysis/files/nptprod.pdb
traj query unit 13

!Open the output file and write header
open write unit 11 card name /home/lherrera/proyectos/charmm/charmm-analysis/files/outleo/rmsd-rgyr-correl.dat
write title unit 11
*#time rmsd rgyr (processed by CORREL)
*

!Invoke CORREL mode
correl maxtime ?nfile

!Now we are in CORREL mode and have access to CORREL subcommands

!request RMS with orient and radius of gyration
enter v1 rms orient
enter v2 gyra

!specify the trajectory and atom selection to process
traj firstu 13 nunit 1 select .not. resn tip3 end

!combine v1 and v2 to allow both time series to be output to one file
edit v1 veccod 2

!write the time series to a file
write v1 dumb time unit 11

! exit CORREL mode
end

stop



output
....
....
....
CHARMM> write title unit 11
RDTITL> *#TIME RMSD RGYR (PROCESSED BY CORREL)
RDTITL> *

CHARMM>

CHARMM> !Invoke CORREL mode
CHARMM> correl maxtime ?nfile
RDCMND substituted energy or value "?NFILE" to "1095649606"

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
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 18645 exclusions and 2239 interactions(1-4)
<MAKGRP> found 762 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 4910265 ATOM PAIRS AND 0 GROUP PAIRS
== PRIMARY == SPACE FOR 7365417 ATOM PAIRS AND 0 GROUP PAIRS

General atom nonbond list generation found:
7313984 ATOM PAIRS WERE FOUND FOR ATOM LIST
404382 GROUP PAIRS REQUIRED ATOM SEARCHES


***** LEVEL -4 WARNING FROM <ALLHP> *****
***** Bad length was passed to FREEHP
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5



/---------\
/ \
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/ \
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! I I I I I !
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-- --
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XXX XXX
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XXX XXX


Execution terminated due to the detection of a fatal error.

ABNORMAL TERMINATION
MAXIMUM STACK SPACE USED IS 307018
STACK CURRENTLY IN USE IS 62
MOST SEVERE WARNING WAS AT LEVEL -4
HEAP PRINTOUT- HEAP SIZE 10240000
SPACE CURRENTLY IN USE IS 7733386
MAXIMUM SPACE USED IS 7733386
FREE LIST
PRINHP> ADDRESS: 1 LENGTH: 2506082 NEXT: 10239469
PRINHP> ADDRESS: 10239469 LENGTH: 532 NEXT: 0

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 2.91 SECONDS
CPU TIME: 2.91 SECONDS


MenB Leonardo David Herrera Zúñiga
POSGRADO EN QUÍMICA UAMI Biofisicoquímica
Universidad Autonoma Metropolitana Iztapalapa
Tel. +52 (55) 5804 4674