Thanks so far. the protein and the one dna strand are now regarded to be one molecule, but it is the wrong strand of the dna and i do not know who to tell pdb2gmx to use not this but the other dna strand which has a 4 bases overlap with which is is bound to the tyrosine OH is there anybody who has a suggestion that may help me fix this ? thank you so much joe
Joern Lenz wrote: > dear guys, > sorry to ask again, but i still have a problem with my simulation and i am very new to gromacs. > my system consists of a protein and a DNA which are covalently connected, i.e. > there is a connecting bond between the P of the DNA backbone and an OH of a tyrosine. > what i have done so far is (thanks prof. van der spoel): i added a line to the specbond.dat file so that this file now looks like: > 6 > CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 > CYS SG 1 HEME FE 2 0.25 CYS2 HEME > CYS SG 1 HEME CAB 1 0.2 CYS2 HEME > CYS SG 1 HEME CAC 1 0.2 CYS2 HEME > HIS NE2 1 HEME FE 1 0.2 HIS1 HEME > TYR OH 1 DGUA P 1 0.16 TYR DGUA > my top file looks like: > #include "ffoplsaa.itp" > #include "blah_A.itp" > #include "blah_B.itp" > #include "spc.itp" > ... > where blah_A.itp is the protein and blah_2.itp is the DNA, so i cannot verify if two atoms, one of DNA and one of protein are connected as i want them to be 'cause they occur in differnt itp files. > in the mailing list i read that i have to add something to the rtp file, too. but what and how (i mean the dna and the protein are in differnt itp files) > so many many thanks for helping in advance you need to rerun pdb2gmx with the specbond.dat file preset. It will now generate the bond and treat your complex as a single molecule and generate a topology for that molecule. > yours > joe > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
