Previous Thread
Next Thread
Print Thread
QM/MM minimization error
#37966 07/09/20 06:40 AM
Joined: Oct 2019
Posts: 22
V
vht Offline OP
Forum Member
OP Offline
Forum Member
V
Joined: Oct 2019
Posts: 22
Dear all,

The following error was obtained for the system of protein with two ligands when running the minimization step of the QM/MM.

***** LEVEL -1 WARNING FROM *****
***** shake already active and may affect fixed atoms
******************************************
BOMLEV ( -1) IS REACHED - TERMINATING. WRNLEV IS 5

The respective .inp and .out files are attached here.Appreciate if you can give a help on this.

Thanks

Attached Files
step_2.minimize_out.txt (36.83 KB, 105 downloads)
SHA1: 4d6ebc462972585d95877fa4b4f1ff19f3c5e8a2
step2_minimize_inp.txt (2.56 KB, 98 downloads)
SHA1: 827d7bb534d2fc0cf9308b205d3dd9ff96162370
Last edited by vht; 07/09/20 06:56 AM.
Re: QM/MM minimization error
vht #37967 07/10/20 01:50 AM
Joined: Sep 2003
Posts: 8,545
Likes: 3
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,545
Likes: 3
One possibility is that the PSF was saved with CONS FIX active for some atoms. If so, adding the following line after reading the .psf file should cure the problem--

CONS FIX SELE NONE END


Rick Venable
computational chemist

Re: QM/MM minimization error
vht #37968 07/10/20 06:14 AM
Joined: Oct 2019
Posts: 22
V
vht Offline OP
Forum Member
OP Offline
Forum Member
V
Joined: Oct 2019
Posts: 22
I did what you suggested but it still giving the same problem. is there any other possibility that I can try?.

Thanks.

Re: QM/MM minimization error
vht #37971 07/10/20 04:26 PM
Joined: Sep 2003
Posts: 8,545
Likes: 3
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,545
Likes: 3
Maybe use an atom selection to limit the scope of the SHAKE command


Rick Venable
computational chemist


Moderated by  BRBrooks, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.014s Queries: 23 (0.008s) Memory: 0.9144 MB (Peak: 1.0029 MB) Data Comp: Off Server Time: 2021-05-08 23:14:46 UTC
Valid HTML 5 and Valid CSS