Yes the error message indicates about the line which is in the very end ( 6 7
2 gb_27). I can see which atoms they are, 6 and 7, but I don`t know how to
solve it??? My part of top file is below, with the line it is complaining about
in bold. Thank you very much.
Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"
#include "H3O.itp"
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
; residue 98 GLU rtp GLUH q 0.0
1 NL 98 GLU N 1 -0.66 14.0067 ; qtot
-0.66
2 H 98 GLU H1 1 0.44 1.008 ; qtot
-0.22
3 H 98 GLU H2 1 0.44 1.008 ; qtot
0.22
4 CH1 98 GLU CA 2 -0.22 13.019 ; qtot 0
5 CH2 98 GLU CB 2 0 14.027 ; qtot 0
6 CH2 98 GLU CG 2 0 14.027 ; qtot 0
7 C 98 GLU CD 3 0.33 12.011 C
0.270126 12.011
8 O 98 GLU OE1 3 -0.45 15.9994 O
-0.634874 15.9994
9 OA 98 GLU OE2 3 -0.288 15.9994 OA
-0.634874 15.9994
10 H 98 GLU HE2 3 0.408 1.008 H
0.000 1.0008
11 C 98 GLU C 4 0.33 12.011 ; qtot
0.33
12 O 98 GLU OT 4 -0.45 15.9994 ; qtot
-0.12
13 OA 98 GLU O 4 -0.288 15.9994 ; qtot
-0.408
14 H 98 GLU HO 4 0.408 1.008 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_2
1 3 2 gb_2
1 4 2 gb_21
4 5 2 gb_27
4 11 2 gb_27
5 6 2 gb_27
6 7 2 gb_27
mehmet
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul
<jalem...@vt.edu>
Sent: Monday, February 10, 2014 4:22 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] free energy calculations for reference state for
constant pH MD simulations...
On 2/10/14, 3:57 PM, Mehmet Ozbil wrote:
> Do you have a suggestion how can I solve it Justin?
>
The error message tells you exactly what the offending line is for the bonded
interaction and you can easily check your math with regards to the charge.
Without seeing the entire topology, I can offer nothing else.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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