Hello Tsjerk, while running pdb2gmx I was getting error like
h1 is not found while assigning improper dihedral so I just modified the forcefield(ffG43a1.rtp)file by default it was considering ADE also inplace of considering DADE part only,so I removed ADE,CYT,GUA part also(is it right to do so?) after that I am not getting any error in this step. Now the topology file that is generated is not having angle type and dihedral type for example: 1.18 19 20(which is nothing but the angle betwen OA P OM) 2.18 19 22(OA P OA) 3.17 18 19 20(CH1 OA P OM) 4.18 19 22 23(OA P OA CH2) then I searched in the ffG43a1bon.itp and get the values llike(I guess it is correct,you please give your suggestion) 1. ga_13(its given for OM P OA) 2.ga_4 (given for same) 3.gd_9 & gd_11 (given for -OA-P-) I added these values to the topology file.It makes the grompp command running I minimized the structure also but the problem I am facing is following: Fatal error: Group other not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Actually gromacs is not recognizing the DNA molecule.while running genbox command I found the following: system is having 1687 :other residue(4 dna and 1683 water molecule) 0:protein 0:dna Now what should I do? I am sure that I am doin something wrong in the beginning itself can you please help me in identifying that error or can you please send me a sample pdb file having dna molecules with regards -- PRASUN (ASHOKA)
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
