Please keep the discussion on the gmx-users mailing list.
On 12/11/12 5:12 PM, Milinda Samaraweera wrote:
Hi Justin
error is
Could only find a forcefield type for 0 out of 2808 atoms
I attached my input files, and I checked .gro for errors. cant find any
I don't exactly know what you've checked, but I think the problem is what I
suggested before - your .gro file specifies atom types instead of valid names.
Your .n2t file cannot match anything.
-Justin
best
Milinda Samaraweera
University of Connecticut
Department of Chemistry
55 N Eagleville road
unit 3060
Storrs CT
USA
--------------------------------------------------------------------------------
*From:* Justin Lemkul <jalem...@vt.edu>
*To:* Milinda Samaraweera <milind...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@gromacs.org>
*Sent:* Tuesday, December 11, 2012 4:59 PM
*Subject:* Re: [gmx-users] g_x2top help
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
========================================
--
========================================
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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