AMBER Archive (2001)

Subject: problem with xleap and sander! (fwd)

From: jim caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Mon Jul 30 2001 - 13:56:23 CDT

---------- Forwarded message ----------
Date: Mon, 30 Jul 2001 11:38:22 -0700 (PDT)
From: PRADIPTA Bandyopadhyay <pradipta_at_cgl.ucsf.edu>
To: amber_at_heimdal.compchem.ucsf.edu
Subject: problem with xleap and sander!

 Hi,

   I am trying to run a minimization ( and MD after that) with my protein
 and ligand system.

 I added 8 Na+ ions using the addions commnad in xleap. My ligand has one
 water molecule. I added waters using the solvateBox command. After I
saved the topology and parameter files I used the ambpdb command to
generate the new pdb file with waters. In the pdb file with water I see
 that three atoms of the water in the ligand are separated by TER while
 TERs between three Na+ disappeared.

 it looks something like this.

TER
ATOM 4093 O44 FOR 264 40.904 37.946 45.599
TER
 ATOM 4094 H45 FOR 264 40.366 37.530 47.200
TER A
ATOM 4095 H46 FOR 264 41.184 38.856 45.700

ATOM 4100 Na+ Na+ 269 52.816 37.228 46.963
 TER
 ATOM 4101 Na+ Na+ 270 42.056 19.000 27.500
ATOM 4102 Na+ Na+ 271 38.913 51.104 56.385
ATOM 4103 Na+ Na+ 272 46.674 43.730 20.284
TER

When I try the 'savepdb' command inside xleap - the pdb file is fine.

So, I am not sure it is a bug of ambpdb or something wrong with my
topology.

However, when I try to run minimization with PME ( using amber6)
It doesn't run. Looking into the PME code, I found that in the
setup_grids subroutine in ew_setup.f - 'cutlist' is zero - which makes
a floating divided by zero.

Why is 'cutlist=0'? Is there any relation between my apparently wrong
topology file and cutlist?

I can run a vacuum minimization with IGB=2.

                                  Pradipta