St�phane, Thank you so much. I will try your suggestion. Yafei ----- Original Message ----- From: [EMAIL PROTECTED] Date: Wednesday, September 5, 2007 6:22 pm Subject: Re: [gmx-users] How to use PRODRG to help new user do gromacs?
> Selon Yafei Dai <[EMAIL PROTECTED]>: > > > Hi, all, > > I am a new user of gromacs and I read the manual and tutorial > but I still get > > confused. > > I need your help. > > > > >From PRODRG, I got four *.top files, one *.itp file and three > *.PDB files > > and some other files. In my system, I don't have any solvents, > no any waters > > and no any ion. > > > > I take the "DRGCNS.TOP : CNS topology file" and "DRGGMX.ITP : > GROMACS .itp > > file" and "DRGFIN.GRO : final coordinates in GROMOS87 format" > to gromacs and > > do "grompp -v", but I get error as below shows: > > > > Fatal error: number of coordinates in coordinate file > (drgfin.gro, 15) > > does not match topology (drgcns.top, 0) > > > > what can I do now? Thank you for you help. > > yafei > > I presume you used the 'standard' proDRG, i strongly recommand to > use the beta > version in order to get parameters for a 'correct' force-field, > like for the > gromos96 and the like. By default (the 2.4 version of proDRG), the > atomdefinitions are provided for ffgmx (aka gromacs or gmx, which > is now deprecated > as stated in the manual). > > Please have a look at http://wiki.gromacs.org/index.php/PRODRG > for further > details. > > Cheers, > > St�phane T�letch�a > > -- > St�phane T�letch�a, PhD. http://www.steletch.org > Unit� Math�matique Informatique et G�nome > http://migale.jouy.inra.fr/migINRA, Domaine de Vilvert > T�l : (33) 134 652 891 > 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting!Please don't post (un)subscribe requests to the list. Use > the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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