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I am using linux.<br>
<br><font face="Arial" size="2"><TABLE STYLE="border-color: blue; border-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD><b><i>-- Original Message --</i></b><br>From: "Wang Zhun " <wangzhun@pumc.edu.cn><br>To: gmx-users@gromacs.org<br>Date: Thu, 29 Dec 2005 22:16:19 +0800<br>Subject: Re:[gmx-users] grompp error!<br><br><br>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?<br><br><br>In your mail:<br>>From: Rahul Karyappa <r.karyappa@ncl.res.in><br>>Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>>To: gmx-users@gromacs.org<br>>Subject: [gmx-users] grompp error!<br>>Date:Thu, 29 Dec 2005 19:00:44 +0530 (IST)<br>><br>>Dear all,<br>><br>> This is my topology file. When I run grompp command it gives me following error :<br>><br>>Fatal error: number of coordinates in coordinate file (out.gro, 7048)does not match topology (topol1.top, 0).<br>><br>><br>>My .top file is as follows:<br>><br>>Please help me out. Thanking you in advance.<br>><br>><br>>Rahul Karyappa<br>><br>><br>><br>>; forcefield parameters<br>><br>>[ defaults ]<br>><br>>; nbfunc <br>>comb-rule <br>>gen-pairs fudgeLJ fudgeQQ<br>><br>>1 <br>>1 <br>>no <br>>1.0 1.0<br>><br>><br>>[ atomtypes ]<br>><br>>;name <br>>mass charge <br>>ptype <br>>c6 c12<br>><br>> OM <br>>15.99940 <br>>-0.736 A <br>>0.22617E-02 0.74158E-06<br>><br>> S <br>>32.06000 <br>>+1.751 A <br>>0.99844E-02 0.13078E-04<br>><br>> OS <br>>15.99940 <br>>-0.736 A <br>>0.22617E-02 0.74158E-06<br>><br>> HC <br>>1.00800 <br>>0.000 A <br>>0.0 0.0<br>><br>> C2 <br>>12.01100 <br>>0.000 A <br>>0.90975E-02 0.35333E-04<br>><br>> C3 <br>>12.01100 <br>>0.000 A <br>>0.88765E-02 0.26150E-04<br>><br>> OW <br>>15.99940 <br>>-0.820 A <br>>0.26171E-02 0.26331E-05<br>><br>> HW <br>>1.00800 <br>>0.410 A <br>>0.00000E+00 0.00000E+00<br>><br>> Na <br>>22.98980 <br>>+1.000 A <br>>0.72059E-04 0.21014E-07<br>><br>> CR6 <br>>12.01100 <br>>0.000 A <br>>0.55132E-02 0.15120E-04<br>><br>> Mg <br>>24.3050 <br>>+1.100 A <br>>0.72059E-04 0.21014E-07<br>><br>> OY1 15.99940 <br>>-0.550 A <br>>0.26171E-02 0.26331E-05<br>><br>> OY2 15.99940 <br>>-0.550 A <br>>0.26171E-02 0.26331E-05<br>><br>> OY3 15.99940 <br>>-0.550 A <br>>0.26171E-02 0.26331E-05<br>><br>> OY4 15.99940 <br>>-0.758 A <br>>0.26171E-02 0.26331E-05<br>><br>> OY5 15.99940 <br>>-0.758 A <br>>0.26171E-02 0.26331E-05<br>><br>> OY6 15.99940 <br>>-0.792 A <br>>0.26171E-02 0.26331E-05<br>><br>> OY7 15.99940 <br>>-0.867 A <br>>0.26171E-02 0.26331E-05<br>><br>> OY8 15.99940 <br>>-0.867 A <br>>0.26171E-02 0.26331E-05<br>><br>> OY9 15.99940 <br>>-0.683 A <br>>0.26171E-02 0.26331E-05<br>><br>> AL1 <br>>26.9815 <br>>+1.450 A <br>>0.72059E-04 0.21014E-07<br>><br>> SI1 <br>>28.0855 <br>>+1.100 A <br>>0.72059E-04 0.21014E-07<br>><br>> SI2 <br>>28.0855 <br>>+1.100 A <br>>0.72059E-04 0.21014E-07<br>><br>> H1 <br>>1.00800 <br>>0.200 A <br>>0.0 0.0<br>><br>> <br>><br>><br>>[ nonbond_params ]<br>><br>> ; i j<br>>func <br>>c6 c12<br>><br>> OM OW 1 0.24329E-02 0.29873E-05<br>><br>> OM Na 1 0.40370E-03 0.44478E-06<br>><br>> OS Na 1 0.40370E-03 0.17791E-06<br>><br>> OW OS 1 0.24329E-02 0.19915E-05<br>><br>> CR6 CR6 1 0.0 0.0<br>><br>><br>>[ pairtypes ]<br>><br>> ; i j<br>>func <br>>cs6 cs12<br>><br>> OM C2 1 0.32685E-02 0.22969E-05<br>><br>> OM OS 1 0.22617E-02 0.74158E-06<br>><br>> OM S 1 0.47520E-02 0.31143E-05<br>><br>> C2 S 1 0.68675E-02 0.96461E-05<br>><br>> C2 OS 1 0.32685E-02 0.22969E-05<br>><br>> C2 C2 1 0.47236E-02 0.71145E-05<br>><br>> C2 C3 1 0.56894E-02 0.92642E-05<br>><br>>; Added manually<br>><br>> HC C2 1 0.0 0.0<br>><br>> HC C3 1 0.0 0.0<br>><br>> HC OS 1 0.0 0.0<br>><br>> HC S 1 0.0 0.0<br>><br>> HC OM 1 0.0 0.0<br>><br>><br>>[ bondtypes ]<br>><br>> ; i j<br>>func <br>>b0 kb<br>><br>> S OM 1 0.15000 376560.<br>><br>> S OS 1 0.15000 376560.<br>><br>> OS C2 1 0.14300 251040.<br>><br>> C2 C2 1 0.15300 334720.<br>><br>> C3 C2 1 0.15300 334720.<br>><br>> C2 HC 1 0.10900 292880.<br>><br>> C3 HC 1 0.10900 292880.<br>><br>> CR6 CR6 1 0.14120 600000.<br>><br>><br>>[ angletypes ]<br>><br>> ; i j k<br>>func <br>>tHC cth<br>><br>> OM S OM 1 109.500 500.080<br>><br>> OM S OS 1 109.500 500.080<br>><br>> S OS C2 1 120.000 397.480<br>><br>> OS C2 C2 1 107.900 460.240<br>><br>> C2 C2 C2 1 111.000 460.240<br>><br>> C2 C2 C3 1 111.000 460.240<br>><br>> HC C2 HC 1 109.500 292.880<br>><br>> C2 C2 HC 1 109.500 292.880<br>><br>> C3 C2 HC 1 109.500 292.880<br>><br>> C2 C3 HC 1 109.500 292.880<br>><br>> OS C2 HC 1 109.500 292.880<br>><br>> HC C3 HC 1 109.500 292.880<br>><br>><br>>[ dihedraltypes ]<br>><br>> ; i l<br>>func <br>>q0 cq<br>><br>> S OS <br>>1 0.000 <br>>3.766 3<br>><br>> OS C2 <br>>1 0.000 <br>>3.766 3<br>><br>> C2 C2 <br>>1 0.000 <br>>5.858 3<br>><br>> C2 C3 <br>>1 0.000 <br>>5.858 3<br>><br>><br>><br>>[ dihedraltypes ]<br>><br>> C2 C2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495<br>><br>><br>><br>><br>><br>><br>>; Include various molecular topologies<br>><br>>#include "1unk.itp"<br>><br>>#include "spc.itp"<br>><br>>#include "1sds.itp"<br>><br>><br>>[ system ]<br>><br>>; Name<br>><br>>unk in water<br>><br>><br>>[ molecules ]<br>><br>>; Compound #mols<br>><br>>unk 1<br>><br>>Na 16<br>><br>>SOL 2148<br>><br>>_______________________________________________<br>>gmx-users mailing list<br>>gmx-users@gromacs.org<br>>http://www.gromacs.org/mailman/listinfo/gmx-users<br>>Please don't post (un)subscribe requests to the list. Use the <br>>www interface or send it to gmx-users-request@gromacs.org.<br><br><br>_______________________________________________<br>gmx-users mailing list<br>gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br><br>*****************************************************************<br>This email is virus free by TrendMicro Inter Scan Security Suite.<br>*****************************************************************<br></TD></TR></tbody></TABLE></font></BODY></HTML>