[gmx-users] g_x2top help
Justin Lemkul
jalemkul at vt.edu
Tue Dec 11 23:21:46 CET 2012
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 <jalemkul at vt.edu>
> *To:* Milinda Samaraweera <milinda49 at yahoo.com>; Discussion list for GROMACS
> users <gmx-users at 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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