From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Apr 18 2005 - 17:23:35 CDT
Hello,
Your questions are interesting. Below you say that the box is 20A, but
yet the cell basis vectors are 100 or more. This is a bit confusing.
Since the basis vectors are greater than the PME grid dimensions by almost
a factor of 2, problems might result. I could be wrong though.
It may also be that the ligand has been cut by the box dimensions with
respect to the PME gridsizes
Just my thoughts...
Brian
On Sat, 16 Apr 2005, E. Davis Oldham wrote:
> 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.
>
************************************************
Brian Bennion, Ph.D.
Bioscience Directorate
Lawrence Livermore National Laboratory
P.O. Box 808, L-448 bennion1_at_llnl.gov
7000 East Avenue phone: (925) 422-5722
Livermore, CA 94550 fax: (925) 424-6605
************************************************
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:21 CST