AMBER: problem about Distance Restraints.

From: Qingning Shu <>
Date: Tue, 11 Jul 2006 23:38:48 -0400

Dear Amber:
I am planing to run a Dynamics with distance restraint between ligand and protein. since my ligand is not standard. I created a new MAP file map.own (add the ligand to the default map file $AMBERHOME/dat/map.DG-AMBER). When I tried to run "makeDIST_RST -ual 8col.wc -pdb my.pdb -map map.own -rst RST.wc", I got a error message. It read "
# makeDIST_RST
Currently configured for up to 5000 atoms
Using MAP file map.own
Assertion failed: nat < MAXATOMS, file makeDIST_RST.c, line 675
Abort (core dumped)
Is my pdb file too big (it is more than 5000 atoms) or something wrong with my map file? What should I do about it?
Thank you in advance.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jul 12 2006 - 06:07:21 PDT
Custom Search