[gmx-users] grompp error!
Rahul Karyappa
r.karyappa at ncl.res.in
Thu Dec 29 14:53:05 CET 2005
I am using linux.
-- Original Message --
From: "Wang Zhun " <wangzhun at pumc.edu.cn>
To: gmx-users at gromacs.org
Date: Thu, 29 Dec 2005 22:16:19 +0800
Subject: Re:[gmx-users] grompp error!
Maybe
you should check the time label and size of your topology files to
select the correct .top file. Something works well in linux does not
apply to windows--are you using the MS Windows port of Gromacs?
In your mail:
>From: Rahul Karyappa <r.karyappa at ncl.res.in>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] grompp error!
>Date:Thu, 29 Dec 2005 19:00:44 +0530 (IST)
>
>Dear all,
>
> This is my topology file. When I run grompp command it gives me following error :
>
>Fatal error: number of coordinates in coordinate file (out.gro, 7048)does not match topology (topol1.top, 0).
>
>
>My .top file is as follows:
>
>Please help me out. Thanking you in advance.
>
>
>Rahul Karyappa
>
>
>
>; forcefield parameters
>
>[ defaults ]
>
>; nbfunc
>comb-rule
>gen-pairs fudgeLJ fudgeQQ
>
>1
>1
>no
>1.0 1.0
>
>
>[ atomtypes ]
>
>;name
>mass charge
>ptype
>c6 c12
>
> OM
>15.99940
>-0.736 A
>0.22617E-02 0.74158E-06
>
> S
>32.06000
>+1.751 A
>0.99844E-02 0.13078E-04
>
> OS
>15.99940
>-0.736 A
>0.22617E-02 0.74158E-06
>
> HC
>1.00800
>0.000 A
>0.0 0.0
>
> C2
>12.01100
>0.000 A
>0.90975E-02 0.35333E-04
>
> C3
>12.01100
>0.000 A
>0.88765E-02 0.26150E-04
>
> OW
>15.99940
>-0.820 A
>0.26171E-02 0.26331E-05
>
> HW
>1.00800
>0.410 A
>0.00000E+00 0.00000E+00
>
> Na
>22.98980
>+1.000 A
>0.72059E-04 0.21014E-07
>
> CR6
>12.01100
>0.000 A
>0.55132E-02 0.15120E-04
>
> Mg
>24.3050
>+1.100 A
>0.72059E-04 0.21014E-07
>
> OY1 15.99940
>-0.550 A
>0.26171E-02 0.26331E-05
>
> OY2 15.99940
>-0.550 A
>0.26171E-02 0.26331E-05
>
> OY3 15.99940
>-0.550 A
>0.26171E-02 0.26331E-05
>
> OY4 15.99940
>-0.758 A
>0.26171E-02 0.26331E-05
>
> OY5 15.99940
>-0.758 A
>0.26171E-02 0.26331E-05
>
> OY6 15.99940
>-0.792 A
>0.26171E-02 0.26331E-05
>
> OY7 15.99940
>-0.867 A
>0.26171E-02 0.26331E-05
>
> OY8 15.99940
>-0.867 A
>0.26171E-02 0.26331E-05
>
> OY9 15.99940
>-0.683 A
>0.26171E-02 0.26331E-05
>
> AL1
>26.9815
>+1.450 A
>0.72059E-04 0.21014E-07
>
> SI1
>28.0855
>+1.100 A
>0.72059E-04 0.21014E-07
>
> SI2
>28.0855
>+1.100 A
>0.72059E-04 0.21014E-07
>
> H1
>1.00800
>0.200 A
>0.0 0.0
>
>
>
>
>[ nonbond_params ]
>
> ; i j
>func
>c6 c12
>
> OM OW 1 0.24329E-02 0.29873E-05
>
> OM Na 1 0.40370E-03 0.44478E-06
>
> OS Na 1 0.40370E-03 0.17791E-06
>
> OW OS 1 0.24329E-02 0.19915E-05
>
> CR6 CR6 1 0.0 0.0
>
>
>[ pairtypes ]
>
> ; i j
>func
>cs6 cs12
>
> OM C2 1 0.32685E-02 0.22969E-05
>
> OM OS 1 0.22617E-02 0.74158E-06
>
> OM S 1 0.47520E-02 0.31143E-05
>
> C2 S 1 0.68675E-02 0.96461E-05
>
> C2 OS 1 0.32685E-02 0.22969E-05
>
> C2 C2 1 0.47236E-02 0.71145E-05
>
> C2 C3 1 0.56894E-02 0.92642E-05
>
>; Added manually
>
> HC C2 1 0.0 0.0
>
> HC C3 1 0.0 0.0
>
> HC OS 1 0.0 0.0
>
> HC S 1 0.0 0.0
>
> HC OM 1 0.0 0.0
>
>
>[ bondtypes ]
>
> ; i j
>func
>b0 kb
>
> S OM 1 0.15000 376560.
>
> S OS 1 0.15000 376560.
>
> OS C2 1 0.14300 251040.
>
> C2 C2 1 0.15300 334720.
>
> C3 C2 1 0.15300 334720.
>
> C2 HC 1 0.10900 292880.
>
> C3 HC 1 0.10900 292880.
>
> CR6 CR6 1 0.14120 600000.
>
>
>[ angletypes ]
>
> ; i j k
>func
>tHC cth
>
> OM S OM 1 109.500 500.080
>
> OM S OS 1 109.500 500.080
>
> S OS C2 1 120.000 397.480
>
> OS C2 C2 1 107.900 460.240
>
> C2 C2 C2 1 111.000 460.240
>
> C2 C2 C3 1 111.000 460.240
>
> HC C2 HC 1 109.500 292.880
>
> C2 C2 HC 1 109.500 292.880
>
> C3 C2 HC 1 109.500 292.880
>
> C2 C3 HC 1 109.500 292.880
>
> OS C2 HC 1 109.500 292.880
>
> HC C3 HC 1 109.500 292.880
>
>
>[ dihedraltypes ]
>
> ; i l
>func
>q0 cq
>
> S OS
>1 0.000
>3.766 3
>
> OS C2
>1 0.000
>3.766 3
>
> C2 C2
>1 0.000
>5.858 3
>
> C2 C3
>1 0.000
>5.858 3
>
>
>
>[ dihedraltypes ]
>
> C2 C2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
>
>
>
>
>
>
>; Include various molecular topologies
>
>#include "1unk.itp"
>
>#include "spc.itp"
>
>#include "1sds.itp"
>
>
>[ system ]
>
>; Name
>
>unk in water
>
>
>[ molecules ]
>
>; Compound #mols
>
>unk 1
>
>Na 16
>
>SOL 2148
>
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