Juliana Angeiras wrote:
Hi,
I'm trying to include parameters of n-butanol in the topology file
(below) (i'm not using opls or other force field for butanol), but when
i run the grompp program, I obtain the following message:
Fatal error:
Atomtype Hb not found
How can I fix this problem?
Your directives are out of order. If you define new atomtypes, etc. they have
to be defined before they can be used. See Chapter 5 of the manual.
-Justin
Thanks
Topology file:
; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"
; Include forcefield parameters
#include "oplsaa.ff/tip5p.itp"
[ moleculetype ]
; name nrexcl
BuOH 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 Hb 1 BuOH HO 1 0.38 1.0080
2 O 1 BuOH OH 1 -0.66 15.9994
3 C 1 BuOH CA 1 0.40 12.0110
4 C 1 BuOH CB 1 -0.22 12.0110
5 C 1 BuOH CC 1 -0.22 12.0110
6 C 1 BuOH CD 1 -0.33 12.0110
7 H 1 BuOH HA 1 -0.06 1.0080
8 H 1 BuOH HB 1 -0.06 1.0080
9 H 1 BuOH HC 1 0.11 1.0080
10 H 1 BuOH HD 1 0.11 1.0080
11 H 1 BuOH HE 1 0.11 1.0080
12 H 1 BuOH HF 1 0.11 1.0080
13 H 1 BuOH HG 1 0.11 1.0080
14 H 1 BuOH HF 1 0.11 1.0080
15 H 1 BuOH HG 1 0.11 1.0080
[ atomtypes ]
; name at.num mass charge ptype V(c6) W(c12)
Hb 1 1.0080 0.38 A 0.4149611E-07 0.9737356E-04
O 8 15.9994 -0.66 A 0.9722461E-06 0.1247853E-02
C 6 12.0110 0.40 A 0.4895634E-05 0.2791672E-02
C 6 12.0110 -0.22 A 0.4895634E-05 0.2791672E-02
C 6 12.0110 -0.33 A 0.4895634E-05 0.2791672E-02
H 1 1.0080 -0.06 A 0.4415162E-06 0.5131711E-03
H 1 1.0080 0.11 A 0.4415162E-06 0.5131711E-03
[ bondtype ]
; ai aj funct c0 c1
HB O 1 0.10900 462750.4
O C 1 0.14300 376560.0
C C 1 0.15300 265265.6
H C 1 0.10800 284512.0
[ angletype ]
; ai aj ak func c0 c1
C O HB 1 108.000 460.240
C C O 1 108.000 418.400
C C C 1 112.000 488.273
H C H 1 109.470 292.000
[ dihedrals ]
1 2 3 4 3 0.41840 1.25520 0.00000 -1.67360 0.00000 0.00000
2 3 4 5 3 2.87441 0.58158 2.09200 -5.54799 0.00000 0.00000
3 4 5 6 3 2.92880 -1.46440 0.20920 -1.67360 0.00000 0.00000
[ nonbond_params ]
; i j func V(c6) W(c12)
H H 1 0.4149611E-07 0.9737356E-04
H HW 1 0.4149611E-07 0.9737356E-04
H C 1 0.4415162E-06 0.5131711E-03
H O 1 0.1927397E-06 0.3416812E-03
H OW 1 0.1927397E-06 0.3416812E-03
H Hb 1 0.4149611E-07 0.9737356E-04
HW HW 1 0.0000000E+00 0.0000000E+00
HW C 1 0.4415162E-06 0.5131711E-03
HW O 1 0.0000000E+00 0.0000000E+00
HW OW 1 0.0000000E+00 0.0000000E+00
HW Hb 1 0.4149611E-07 0.9737356E-04
C C 1 0.4895634E-05 0.2791672E-02
C O 1 0.2159724E-05 0.1866537E-02
C OW 1 0.2159724E-05 0.1866537E-02
C Hb 1 0.4415162E-06 0.5131711E-03
O O 1 0.9722461E-06 0.1247853E-02
O OW 1 0.1562282E-05 0.1785000E-02
O Hb 1 0.0000000E+00 0.0000000E+00
OW OW 1 0.2510400E-05 0.2552000E-02
OW Hb 1 0.0000000E+00 0.0000000E+00
Hb Hb 1 0.4149611E-07 0.9737356E-04
[ system ]
; Name
BuOH in water
[ molecules ]
; Compound #mols
BuOH 343
SOL 185
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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