I think I answered this a couple days ago, or a very similar question.
Try searching the list.
David
On 8/7/06, Owen, Michael <[EMAIL PROTECTED]> wrote:
Hello,
I am trying to use NMR restraints to position a Cu2+ ion around specific
residues of a peptide. I added Cu2+ using "genion" and then initiated
"grompp" before an energy minim minimization. I received the following
error message while executing "grompp":
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 1108
Fatal error:
[ file "Ab_Cu.top", line 5864 ]:
Atom index (67248) in distance_restraints out of bounds (1-1)
-------------------------------------------------------
Below is the entry in the topology file. Line 5864 contains the value 97
and the value 67248 refers is the atom number of the Cu2+ ion.
[ distance_restraints ]
;ai aj type index type' low up1 up2 fac
67248 97 1 1 1 0.185 0.195 0.2 1.0
67248 196 1 1 1 0.185 0.195 0.2 1.0
67248 213 1 1 1 0.185 0.195 0.2 1.0
67248 148 1 1 1 0.195 0.205 0.21 1.0
Could you suggest any changes that would eliminate my error?
Thanks in advance,
Michael Owen
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
