Well, I figured out the problem. I prepared a new prmtop file. Now it works fine..
Thank you
Cenk Andac, M.S., Ph.D.
--- On Sun, 12/5/10, Cenk (Jenk) Andac <cenk_andac.yahoo.com> wrote:
From: Cenk (Jenk) Andac <cenk_andac.yahoo.com>
Subject: [AMBER] problem with entropy computations by mm_pbsa_nabnmode
To: amber.ambermd.org
Date: Sunday, December 5, 2010, 3:17 AM
Hi I would like to test entropy computations by the `mm_pbsa_nabnmode` module of amber11. I have a 10 ns MD trajectory for small 11-aa peptide. I extracted 1 snapshot (in pdb format) between 9ns and 10ns of the MD trajectory and implimented the following command.
mm_pbsa_nabnmode mol.pdb ./mol_mmpbsa.prmtop "ntpr=50, nsnb=999999, cut=999., diel=C, gb=1, rgbmax=999., gbsa=1, surften=0.0072, epsext=80.0, kappa=0" 10000 0.5 > mm_pbsa_nabnmode.out 2>&1
However, I keep getting the following error message in the output file.
Reading parm file (./mol_mmpbsa.prmtop)
title:
mm_options: ntpr=50
mm_options: nsnb=999999
mm_options: cut=999.
mm_options: diel=C
mm_options: gb=1
mm_options: rgbmax=999.
mm_options: gbsa=1
mm_options: surften=0.0072
mm_options: epsext=80.0
mm_options: kappa=0
bad number of bonds to C: 259 1; using default carbon parameters
bad number of bonds to C: 809 1; using default carbon parameters
bad number of bonds to C: 977 1; using default carbon parameters
bad number of bonds to C: 1110 1; using default carbon parameters
bad number of bonds to C: 1635 1; using default carbon parameters
bad number of bonds to C: 1726 1; using default carbon parameters
bad number of bonds to C: 1809 1; using default carbon parameters
bad number of bonds to C: 1842 1; using default carbon parameters
bad number of bonds to C: 2422 1; using default carbon parameters
bad number of bonds to C: 2502 1; using default carbon parameters
bad number of bonds to C: 3121 1; using default carbon parameters
bad number of bonds to C: 3258 1; using default carbon parameters
Can someone please let me know what I am doing wrong?
best regards,
Jenk
Cenk Andac, Ph.D.
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Received on Sun Dec 05 2010 - 03:30:03 PST
