From: E. Davis Oldham (eoldham2_at_uiuc.edu)
Date: Sat Apr 16 2005 - 12:37:37 CDT
Hi everybody-
I'm fairly new to namd, and I don't know much about
computational biochemistry. I'm trying to minimize a crystal
structure of diethylstilbestrol (DES) bound to the ligand
binding domain (LBD) of the estrogen receptor. I have
successfully minimized just the estrogen receptor, but when
I try to do it with DES in the crystal structure, I get
several errors.
ERROR: Stray PME grid charges detected: 4 sending to 6 for
planes 35
ERROR: Stray PME grid charges detected: 2 sending to 6 for
planes 35
ERROR: Stray PME grid charges detected: 3 sending to 6 for
planes 35
...
Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid
this.
Warning: Stray PME grid charges ignored!
...
UX:cp: ERROR: testtestttest - No such file or directory
The output also says that I have created output files that
have in fact not been placed in the output directory.
The receptor is in a 20 Angstrom box, with
Info: PERIODIC CELL BASIS 1 100 0 0
Info: PERIODIC CELL BASIS 2 0 100 0
Info: PERIODIC CELL BASIS 3 0 0 107
Info: PERIODIC CELL CENTER 11 -2 7
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.190674
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 62 62 62
Please help.
Thank you very much,
Davis Oldham
Grad student @ UIUC
Chemistry Dept.
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