----- Original Message ----- From: Tsjerk Wassenaar <[EMAIL PROTECTED]> Date: Saturday, February 16, 2008 6:03 pm Subject: Re: [gmx-users] How to ask pdb2gmx to print all parameters in the itp file To: Discussion list for GROMACS users <[email protected]>
> Hi, > > grompp allows you to write the (cpp) processed topology (-pp). Since > many parameters are controlled using cpp #define statements, cpp has > to be called to fill the values. pdb2gmx can't do that. The OP wanted a tool to do more than #include, they also wanted something to perform mapping of interaction functions from atom numbers to atom types to parameters. The only straightforward way to do this is via grompp. Either use gmxdump on the .tpr file resulting from grompp and parse the output (remember that numbering now starts at zero, whereas in the .top it starts at 1), or write a new output module for grompp to do what you want it to do, or write a new program to parse the .tpr file, since you can re-use a lot of existing code from mdrun which has to do the same task. Mark > On Feb 15, 2008 6:46 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > > If you convert the tpr binary into a text file, it should have > every parameter in it I think? > > > > > > ----- Original Message ---- > > From: LeeHui <[EMAIL PROTECTED]> > > To: [email protected] > > Sent: Friday, February 15, 2008 4:57:13 PM > > Subject: [gmx-users] How to ask pdb2gmx to print all > parameters in the itp file > > > > > > Dear all gmx users, > > > > I am converting the parameters in "itp" file into DL_POLY > format, and will be using it in my own version of DL-poly. > > I was wondering if there is a way to ask pdb2gmx or some other > utilities in Gromacs to print all the parameters into itp, so I > don't have go to the database and find them out. > > > > eg. the default pdb2gmx generated itp have this format > > [ angles ] > > ; ai aj ak > funct c0 c1 c2 c3 > > 1 > 2 3 1 > > 1 > 2 4 1 > > 1 > 2 5 1 > > 3 > 2 4 1 > > > > instead of leaving c0, c1.. blank, I want the exact values of > them printed . > > > > Is there a way to this in Gromacs ? > > > > > > Thanks, > > > > > > Hui > > _________________________________________________________________ > > Windows Live Photo gallery 数码相机的超级伴侣，轻松管理和编辑照片，还能制作全景美图！ > > http://get.live.cn/product/photo.html > > _______________________________________________ > > 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 > > > > > > > ____________________________________________________________________________________> > Looking for last minute shopping deals? > > Find them fast with Yahoo! Search. > http://tools.search.yahoo.com/newsearch/category.php?category=shopping> > > _______________________________________________ > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623> _______________________________________________ > 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 _______________________________________________ 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
