On Mon, Oct 5, 2009 at 4:39 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Francesco Pietra wrote: >> >> 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. >> ============ >> > > Then you haven't yet appropriately #included the .itp file for DPPC.
As I said, I don't understand why about DPPC. The protein is pure standard amino acids and nothing else. I am trying to get the files for simulation in vacuum. I have reexamined all the stuff and I don't see any allusion to a bilayer, unless that comes from the .mdp file. The .top I used in these last attempts reads: ; ; mod21 | MARTINI 2.1 ; ; Include force field poarameters 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" ; Define a name for your system [ system ] mod21 ; Define the composition of your system ; The molecule names should correspond to those defined in the itp file(s). [ molecules ] Protein 1 ; DPPC 128 ; W 2000 ; NA+ 20 ; CL- 20 It seems that commenting out ";" is placed correctly. I am sincerely sorry to bother you again. francesco > >> 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? >> > > Non-matching names occur because MARTINI doesn't assign them correctly in > the initial system setup. Using the .top names is fine. > > The I/O error comes from the fact that you have passed the -n flag to grompp > without having index.ndx in the working directory. Note that having an > index file doesn't necessarily solve your problem; the warning is printed in > case you have non-default groups for, e.g., T-coupling or energygrps. If > you have a "moleculetype not found," then you haven't #included the .itp > file and an index file won't save you. > > -Justin > >> >> 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 >>> >>> >> > > -- > ======================================== > > 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. 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