VMD-L Mailing List
From: larac_at_berkeley.edu
Date: Tue Feb 15 2011 - 18:23:57 CST
- Next message: John Stone: "VMD 1.9 beta 1 posted for download..."
- Previous message: snoze pa: "DOPC membrane"
- In reply to: Axel Kohlmeyer: "Re: setting different bond length for different atom pair"
- Next in thread: Debasis Sengupta: "Re: setting different bond length for different atom pair"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hi,
I am having 2 issues when running volmap ils.
1. What is the difference between the -conf and -orient function? Is one
supposed to replace the other? If I would like the probe to be evaluated
in 50 different rotational orientations, should I specify -conf 50 or
-orient n with n = ?.
2. I get the following error:
ERROR) Found invalid VDW parameters 12: occupancy=-0.000000, radius=0.000000
when using the command:
volmap ils 0 {{-68 -77 -80} {68 77 80}} -cutoff 12.0 -res 1 -subres 3
-alignsel $sel -maxenergy 87 -T 300 -probecoor {{0.00 0.00 0.00} {0.00
1.23 0.00}} -probevdw {{-0.12 1.7} {-0.12 1.7}} -dx output.dx
My command specifies the VDW parameters of my probe and I have
loaded/assigned an AMBER parameter file previously, so I am not sure what
the problem is. Is there a way to get more information about what is
missing?
Thank you very much,
Lara
- Next message: John Stone: "VMD 1.9 beta 1 posted for download..."
- Previous message: snoze pa: "DOPC membrane"
- In reply to: Axel Kohlmeyer: "Re: setting different bond length for different atom pair"
- Next in thread: Debasis Sengupta: "Re: setting different bond length for different atom pair"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]