The answers to both of these questions are in the comments in src/kernel/toppush.c, in function push_at(). I found them grepping src/*/*.[ch] for scanf (the C function you'd use to read up these files) and looking for topology-related filenames...
> I'd like to use oplsaa FF format to build my own force field for my > project. After I finished it, I can use pdb2gmx. but not grompp. The > problem is from my **nb.itp file. I have specified some unusual (not > follow the combination rule) nonbonded interaction parameters after > [ atomtypes ] section as follows: > > [ nonbond_params ] > ; i j func sigma epsilon > CT CT 1 3.80000e-01 2.09200e-01 > > When I run grompp, the program complains that atom type CT is not found. > If I change CT to opls_182, then it works fine. However, when I check > oplsaabon.itp, CT is used, but not opls_182. Could anyone tell me why I > can't use atom type in *nb.itp? How can I fix it? If opls_182 is defined > as atom type, then how does gromacs recognize CT is **bon.itp? OPLS/AA appears to use different names for bonded and non-bonded atom types. See line 172 of the above file. > By the way, my question relates to my previous question. Unfortunately, > no one answered it. I really appreciate someone can help me. The > following is my previous email: > > In ffoplsaanb.itp, there are 8 columns. > ; name bond_type mass charge ptype sigma epsilon > opls_001 C 6 12.01100 0.500 A 3.75000e-01 > 4.39320e-01 ; SIG > > In ffG53a5nb.itp, there are 7 columns. > [ atomtypes ] > ;name at.num mass charge ptype c6 c12 > O 8 0.000 0.000 A 0.0022619536 1e-06 > > Could anyone tell me how gromacs knows to read 8 columns for oplsaa FF, > but 7 columns for gromos FF? Thanks! The algorithm is described just below in that file too. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
