hi, all Finally figured out that it was because all numbers in the cmap.itp file must be separated by only one space,otherwise the program will read in a "zero". I would suggest this to be fixed in the release version.
have a nice day. dawei On Tue, Jun 29, 2010 at 9:05 AM, Da-Wei Li <[email protected]> wrote: > It is because I want to apply cmap to my own stuff. I can define my > own 2D grid potential and apply to two sequential dihedral angles by > add one line in the topol file. However, the testing result is really > unexpected. > > dawei > > On Tue, Jun 29, 2010 at 8:53 AM, Per Larsson <[email protected]> wrote: >> Hi, >> >> I do not fully understand what you are trying to do, but currently CMAP is >> only >> available for the standard amino acid residues present in the rtp-file for >> the >> Charmm-forcefield, and the values for the grid are specified in the >> cmap.itp-file. >> >> Do you use something else? >> >> /Per >> >> >> 29 jun 2010 kl. 14.45 skrev Da-Wei Li: >> >>> HI, David, >>> >>> thanks for your advise. I remove the bond angle force and get same >>> result. It is really strange. If I set +5 on all the 24*24 grid, I >>> just get a inverted distribution and if I set 0 on all grid, I will >>> get a uniformed distribution. It is like that 27 regions are force to >>> have zero cmap potential. I cannot attach figure due to size limit the >>> list. I have sent the figure to you directly. >>> >>> best, >>> >>> dawei >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.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://lists.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://lists.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
