On 12/11/12 4:40 PM, Milinda Samaraweera wrote:
Hi Gromacs users
I have a problem Im trying to form a .top file using a g_x2top -f -o -ff
command. I have defined .n2t .rtp .itp files. and wanted to construct a
topology file. but the script does not identify any of the atoms from .gro file.
my .n2t file
; clayff
; n2t
H h* 0.4100 1.008 1 O 0.100 ;water hydrogen
H ho 0.4250 1.008 1 O 0.100 ;hydrxyl hydrogen
O o* -0.8200 15.998 2 H 0.100 H 0.100 ;water oxygen
O oh -0.9500 15.998 1 H 0.100 ;hydroxyl oxygen
O ob -1.0500 15.998 0 ;bridging oxygen
O obos -1.1808 15.998 0 ;bridging oxygen with
octahedral substitution
O obts -1.1688 15.998 0 ;bridging oxygen with
tetrahedral substitution
O obss -1.2996 15.998 0 ;bridging oxygen with double
substitution
O ohs -1.0808 15.998 1 H 0.100 ;hydroxyl hydrogen with
substitution
Si st 2.1000 28.086 0 ;tetrahedral silicon
Al ao 1.5750 26.982 0 ;octahedral aluminium
Al at 1.5750 26.982 0 ;tetrahedral aluminium
Mg mgo 1.3600 24.305 0 ; octahedral magnisium
Na Na 1.0000 22.999 0 ;sodium ion
my.itp file
;
;
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
; parameters are taken from the clay force field
[ atomtypes ]
; The charges here will be overwritten by those in the rtp file
; name mass charge ptype sigma eps
h* 1 1.00800 0.4100 A 0.00000e-01 0.00000e-01
;clayFF_waterhydrogen
ho 1 1.00800 0.4250 A 0.00000e-01 0.00000e-01
;clayFF_hydroxylhydrogen
o* 8 15.99800 -0.8200 A 3.16557e-01 6.50209e-01
;ClayFF_wateroxygen
oh 8 15.99800 -0.9500 A 3.16557e-01 6.50209e-01
;ClayFF_hydroxyloxygen
ob 8 15.99800 -1.0500 A 3.16557e-01 6.50209e-01
;ClayFF_bridgingoxygen
obos 8 15.99800 -1.1808 A 3.16557e-01 6.50209e-01
;ClayFF_bridgingoxygenoctasub
obts 8 15.99800 -1.1688 A 3.16557e-01 6.50209e-01
;ClayFF_bridgingoxygentetrsub
ohs 8 15.99800 -1.0808 A 3.16557e-01 6.50209e-01
;ClayFF_hydroxyloxygensub
st 14 28.08600 2.1000 A 3.30208e-01 8.0e-06
;ClayFF_tetrahedralsilicon
ao 13 26.98200 1.5750 A 4.27128e-01 6.0e-06
;ClayFF_octahedalaluminium
at 13 26.98200 1.5750 A 3.30206e-01 8.0e-06
;ClayFF_tetrasubaluminium
mgo 12 24.30500 1.3600 A 5.26437e-01 4.0e-06
;ClayFF_octasubmagnisium
Na 11 22.999 1.0000 A 1.89744e-01 6.72427e-01 ;ClayFF_Na
[ bondtypes ]
; i j func b0 kb
oh ho 1 0.10000 463711.2 ; O-H
ohs ho 1 0.10000 463711.2 ; O-H
o* h* 1 0.10000 463711.2 ; O-H
[ angletypes ]
ao oh ho 1 109.470 251.046 ; angle Al-O-H
mgo ohs ho 1 109.470 251.046 ; angle Mg-O-H
h* o* h* 1 109.470 383.009 ; angle H-O-H
[ dihedraltypes ]
my .gro file
1Created by VESTA
2808
Clay ao 1 0.005 0.564 -0.021
Clay ao 2 -0.602 0.564 3.099
Clay ao 3 4.226 0.564 -0.021
Clay ao 4 3.620 0.564 3.099
Clay st 5 0.178 0.254 0.256
Clay ob 6 0.175 0.240 0.090
Clay ob 7 0.201 0.411 0.296
Clay ob 8 0.037 0.622 0.318
Clay oh 9 0.192 -0.046 0.090
Clay oh 10 0.192 3.610 0.090
Clay ho 11 0.099 -0.046 0.151
Clay ho 12 0.099 3.610 0.151
Clay st 13 0.058 0.254 1.263
Clay ob 14 0.061 0.240 1.429
Clay ob 15 0.035 0.411 1.222
Clay ob 16 0.199 0.622 1.200
Clay oh 17 0.044 -0.046 1.429
Clay oh 18 0.044 3.610 1.429
Clay ho 19 0.136 -0.046 1.368
Clay ho 20 0.136 3.610 1.368
Clay ao 21 0.005 0.259 -0.021
Clay ao 22 -0.602 0.259 3.099
Clay ao 23 4.226 0.259 -0.021
Clay ao 24 3.620 0.259 3.099
Clay st 25 0.058 0.568 1.263
Clay ob 26 0.061 0.582 1.429
Clay ob 27 0.199 0.200 1.200
Clay st 28 0.178 0.568 0.256
Clay ob 29 0.175 0.582 0.090
Clay ob 30 0.037 0.200 0.318
Clay ao 31 0.268 0.107 -0.021
Clay ao 32 -0.338 0.107 3.099
could any one please let me know what might be the problem
Well what error do you get? There are a number of possible issues, but without
knowing what the problem is, it's all guesswork. Potential issues:
1. In place of atom names in the .gro file, you're using atom types
2. The .gro file does not have residue numbers anywhere (see
http://manual.gromacs.org/online/gro.html)
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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