Thanks Justin, Here I pasted water.top
; ; File 'water.top' was generated ; By user: ndhumal (36026) ; On host: c63 ; At date: Thu Apr 21 14:52:38 2011 ; ; This is your topology file ; Protein ; ; Include forcefield parameters #include "ffoplsaa.itp" ; Include water topology ;#include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions ;#include "ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols SOL 256 Nilesh On Thu, April 21, 2011 8:03 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> I am trying to run a simulation for flexiable water. I use the >> parameters from J. Chem. Phys. (2006),124,024503 paper and made a >> spc_fw.itp file. >> >> ; Derived from parsing of runfiles/alat.top.orig >> [ defaults ] >> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >> ;1 3 yes 0.5 0.5 >> ; comb-rule 3 is square-root sigma, the OPLSAA version >> >> >> [ atomtypes ] >> ; full atom descriptions are available in ffoplsaa.atp >> ; name bond_type mass charge ptype sigma epsilon >> opls_116 OW 8 9.95140 -0.820 A 3.165492e-01 >> 6.50299455e-01 >> opls_117 HW 1 4.03200 0.410 A 0.00000e+00 >> 0.00000e+00 >> >> >> [ bondtypes ] >> ; i j func b0 kb >> OW HW 1 1.012 443153.3808 ; J. Chem. Phys. >> (2006),124,024503 >> >> >> >> [ angletypes ] >> ; i j k func th0 cth >> HW OW HW 1 113.24 317.5656 ; J. Chem. Phys. >> (2006),124,024503 >> >> >> >> I am geting the error for >> >> >> grompp -f minim.mdp -c water.pdb -p water.top -o 1.tpr >> >> >> error I am getting >> >> rogram grompp, VERSION 4.0.7 Source code file: topio.c, line: 415 >> >> >> Fatal error: >> Syntax error - File water.top, line 26 >> Last line read: >> '[ system ]' >> Invalid order for directive system >> >> >> How can I fix this error? >> >> > > Assemble the components of your .top in the correct order, as described > in chapter 5 of the manual. Without seeing the contents of "water.top" > that's the best anyone can offer. > > -Justin > > >> Nilesh >> >> >> >> >> > > -- > ======================================== > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
