AMBER Archive (2004)

Subject: AMBER: Leap atom removal bug?

From: david.evans_at_ulsop.ac.uk
Date: Thu Mar 04 2004 - 04:30:01 CST

Dear all,

I need to use leap to remove a large number of atoms from a structure, before reading in another PDB file and generating prmtop and prmcrd file. (I'm creating a ligand covalently bound to DNA).

I would like to do this in a script (leap.in file), but I have found that
leap crashes with a segmentation fault if I try to remove an atom (using 'remove' text command) when it is bonded to any other atom. If I remove all the relevant bonds ('deletebond') first, so that the atom is isolated, then the 'remove' command works. But identifying all the bonds correctly is a bit tedious, and not easily transferrable to other molecules, which was the point of using a script.

I guess that this is a bug otherwise there would be no seg fault. Presumably it is the desired behaviour that removing an atom also removes all bonds to it. If anyone can suggest an alternative approach, or is interested in trying to fix the bug, then I'd be very grateful.

I am using AMBER7 on RedHat 9, compiled with ifort8+gcc3.2.2

Dave Evans
London School of Pharmacy


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