Thanks, and beg pardon for the pedestrian mistake. However, I am not yet out. .tpr not generated
With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -o mod21.cg.tpr There are: 0 OTHER residues There are: 1270 PROTEIN residues There are: 0 DNA residues Analysing Protein... ------------------------------------------------------- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 798 Fatal error: Group DPPC not found in indexfile. Maybe you have non-default groups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. As I said before, I am using the mdp file as provided by MARTINI. ============ With command $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top -n -o mod21.cg.tpr NOTE: System has non-zero total charge: -5.000000e+01 processing coordinates... Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCQd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BSP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SSAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCC3 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BCP5 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCN0 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SCQd - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHN0 - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHAC1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (BHNd - BN0) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC2) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSP1 - SC1) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC3) Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't match (SHSC4 - SC4) (more than 20 non-matching atom names) WARNING 2 [file "mod21.cg.top", line 28]: 2875 non-matching atom names atom names from mod21.cg.top will be used atom names from mod21.cg.box.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 2724 # G96ANGLES: 2860 # PDIHS: 328 # IDIHS: 187 # CONSTR: 745 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... ------------------------------------------------------- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/gmxlib/futil.c, line: 345 File input/output error: index.ndx ========== Non-matching because of the many -S-S- bonds? Why asking about index.ndx? Thanks for help francesco On Mon, Oct 5, 2009 at 12:33 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Francesco Pietra wrote: >> >> Hi: >> >> As I found it difficult to manage solvation - the way I would like - >> with a pore protein (a trimer) partly immersed into a bilayer, I >> started with the protein alone in vacuum, in order to try to fix the >> problems step-by-step. Unfortunately, I can't fix simple problems with >> grompp. >> >> 1) Generated mod21.itp from mod21.pdb >> >> 2) Generated mod21.cg.pdb with awk script) >> >> 3) editconf -f mod21.cg.pdb -o mod21.cg.gro >> >> 4) genbox -cp mod21.cg.gro -box 10 17 10 -o mod21.cg.box.gro >> >> 5) grompp -np 4 -f mod21.cg.box.mdp -c mod21.cg.box.gro -p >> mod21.cg.box.top -warnmax 10 >> >> Error: no such moleculetype Protein. >> >> ............................. >> .mdp is merely a renamed martini_v2.0.example.mdp, taking care that >> "cpp = /usr/bin/cpp". >> >> .top was from editing martini_v2.0.example.top and reads (in between ===): >> ====== >> ; >> ; mod21 | MARTINI 2.1 >> ; >> >> ; Include force field parameters containing all particle definitions, >> ; the interaction matrix, plus the topology for water. >> >> #include "martini_v2.1.itp" >> >> ; Then include the file(s) containing the topologies of other >> ; molecules present in your system. >> >> ; #include "martini_v2.0_lipids.itp" >> ; #include "martini_v2.0_salt.itp" >> >> #include mod21.itp >> > > This #include statement has the wrong syntax. See any of the above for the > correct way to do it. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
