AMBER: RE: AMBER :LINMIN problem

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 17 Jun 2005 11:27:25 -0700

Dear Varsha,

> Dear Ross, i am having LINMIN FAILURE trouble while

> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 1 NaN NaN 4.5414E+06
> CA 2569
>
> BOND = 786.7016 ANGLE = 1486.0724
> DIHED = 2287.6525
> VDWAALS = NaN EEL = NaN
> HBOND = 0.0000
> 1-4 VDW = 1208.7947 1-4 EEL = 12934.5121
> RESTRAINT = 0.0000
>
> .... RESTARTED DUE TO LINMIN FAILURE ...

Your Van Der Waals energy and electrostatic energy is infinite. Thus there
is almost certainly something wrong with your structure. Open it in
something like VMD and take a look. Also try the 'check' command in leap.
You probably have two atoms sitting on top of each other.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Jun 17 2005 - 19:53:00 PDT
Custom Search