>Tom, > >Now before anything else..., do you need a CB to be defined? Doesn't >one of the atom types present suffice? There's tyrosine in most force >field already, you know, and these 'CB' atoms are merely part of the >ring.
Indeed. If I just replace the CB and CR61 by C in the rtp file and add the bondtypes using the G53a6bon.itp then PTR is defined as follows [ PTR ] [ atoms ] ; name type charge chargegroup O2P OA -1.099 1 P P 1.162 1 O3P OA -1.099 1 O1P OM -0.786 1 OH OA -0.178 1 CZ C 0.077 2 CE2 C -0.038 2 CD2 C -0.039 2 CE1 C -0.029 3 CD1 C -0.029 3 CG C 0.002 3 CB CH2 0.056 3 CA CH1 0.184 4 C C 0.436 4 O O -0.546 4 N NL 0.835 4 [ bonds ] O2P P gb_28 P O3P gb_28 P O1P gb_24 P OH gb_28 OH CZ gb_13 CZ CE2 gb_16 CZ CE1 gb_16 CE2 CD2 gb_16 CD2 CG gb_16 CE1 CD1 gb_16 CD1 CG gb_16 CG CB gb_27 CB CA gb_27 CA C gb_27 CA N gb_21 C O gb_5 Then I get again an error for the command -bash-3.00$ grompp -f em.mdp -c sh2_pep_b4em.gro -p sh2_pep.top -o sh2_pep.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations WARNING 1 [file "sh2_pep.top", line 2378]: No default G96Bond types, using zeroes WARNING 2 [file "sh2_pep.top", line 2379]: No default G96Bond types, using zeroes WARNING 3 [file "sh2_pep.top", line 2380]: No default G96Bond types, using zeroes WARNING 4 [file "sh2_pep.top", line 2381]: No default G96Bond types, using zeroes WARNING 5 [file "sh2_pep.top", line 2382]: No default G96Bond types, using zeroes WARNING 6 [file "sh2_pep.top", line 2383]: No default G96Bond types, using zeroes WARNING 7 [file "sh2_pep.top", line 2384]: No default G96Bond types, using zeroes WARNING 8 [file "sh2_pep.top", line 2385]: No default G96Bond types, using zeroes WARNING 9 [file "sh2_pep.top", line 2386]: No default G96Bond types, using zeroes WARNING 10 [file "sh2_pep.top", line 2387]: No default G96Bond types, using zeroes Cleaning up temporary file grompp6oaBPr ------------------------------------------------------- Program grompp, VERSION 3.3 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated ------------------------------------------------------- "It's Because Of the Metric System" (Pulp Fiction) _______________________________________________ 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