AMBER: Leap atom removal bug?

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Date: Thu, 4 Mar 2004 10:30:01 +0000

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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).=20

I would like to do this in a script ( 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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Received on Thu Mar 04 2004 - 10:53:00 PST
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