Dear all My system contains protein + cnt + water molecules.
I have summarized what I did below: ----------------------------------------------------------------------------------- 1) By pdb2gmx and charmm27 force field, I obtained pr.top for protein then I converted it into pr.itp by deleting ; Include forcefield parameters #include "charmm27.ff/forcefield.itp" from begining of file and by deleting ; Include water topology #include "charmm27.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "charmm27.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 from ending of file. ------------------------------------------------------------------------------------ 2) I used bonded and nonbonded parameters for cnt from paper: J. Phys. Chem. B 2001, 105, 9980-9987 (Carbon Nanotubes in Water: Structural Characteristics and Energetics). I created cnt.ff folder containing following files: ffcnt.atp / ffcnt.n2t / ffcnt.rtp / ffcntbon.itp / ffcntnonbon.itp / forcefield.itp Then, I put cnt.ff folder in GMXLIB directory. ------------------------------------------------------------------------------------ 3) By g_x2top and cnt.ff created in previous step, I obtained cnt.top for cnt then I converted it into cnt.itp by deleting ; Include forcefield parameters #include "cnt.ff/forcefield.itp" from begining of file and by deleting [ system ] ; Name CNT [ molecules ] ; Compound #mols CNT 1 from ending of file. ------------------------------------------------------------------------------------ 4) I combined cnt and protein to create one coordination file (system.gro). Order of molecules are as follows: 1) cnt 2) protein 3) water. ------------------------------------------------------------------------------------ 5) I wrote a topol.top file given below, ; Include forcefield parameters #include "cnt.ff/forcefield.itp" #include "cnt.itp" #include "charmm27.ff/forcefield.itp" #include "pr.itp" ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "charmm27.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "charmm27.ff/ions.itp" [ system ] ; Name CNT/Protein/SOL [ molecules ] ; Compound #mols CNT 1 Protein 1 SOL 1359 ------------------------------------------------------------------------------------ When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I encountered with following error: Fatal error: Syntax error - File forcefield.itp, line 11 Last line read: '[ defaults ]' Invalid order for directive defaults Content of forcefield.itp in cnt.ff directory is as follows: ******************************************************************************* * CHARMM port writted by * * Par Bjelkmar, Per Larsson, Michel Cuendet, * * Berk Hess and Erik Lindahl. * * Correspondance: * * bjelk...@cbr.su.se or lind...@cbr.su.se * ******************************************************************************* #define _FF_CNT [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 #include "ffcntnonbon.itp" #include "ffcntbon.itp" and Content of forcefield.itp in Charmm27.ff directory is as follows: ******************************************************************************* * CHARMM port writted by * * Par Bjelkmar, Per Larsson, Michel Cuendet, * * Berk Hess and Erik Lindahl. * * Correspondance: * * bjelk...@cbr.su.se or lind...@cbr.su.se * ******************************************************************************* #define _FF_CHARMM [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 #include "ffnonbonded.itp" #include "ffbonded.itp" #include "gb.itp" #include "cmap.itp" ; Nucleic acids nonbonded and bonded parameters" #include "ffnanonbonded.itp" #include "ffnabonded.itp" ------------------------------------------------------------------------------------ In both of forcefield.itp files, line 11 is [ defaults ]. I changed name of forcefield.itp file in cnt.ff directory to cntff.itp, but there is same error, again. That is all what I exactly did. Is anything wrong or missing? How to solve this error? Any help will highly appreciated -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
