Re: [gmx-users] Invalid order for directive defaults
On 11/13/13 11:53 AM, Atila Petrosian wrote: Dear Justin Thanks for your quick reply. I was confused. If I add #include "ffcntbon.itp" after #include "cnt.itp" in .top file, my problem was solved and error was solved? No. The parameters are at the force field level and thus have to be #included before any [moleculetype] is introduced (see Chapter 5 of the manual for required order of directives). If you do: #include "charmm27.ff/forcefield.itp" #include "ffcntbon.itp" you should be fine. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
[gmx-users] Invalid order for directive defaults
Dear Justin Thanks for your quick reply. I was confused. If I add #include "ffcntbon.itp" after #include "cnt.itp" in .top file, my problem was solved and error was solved? -- gmx-users mailing listgmx-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
Re: [gmx-users] Invalid order for directive defaults
On 11/13/13 10:39 AM, Atila Petrosian wrote: Dear Justin Thanks for your reply. In your previous setup, you were effectively trying to use CHARMM27 + some other force field related to the CNT. You can't do that. Thus, Gromacs is not appropriate for systems containing cnt. Is my deduction true? Of course not. People simulate CNTs with Gromacs all the time. You just didn't construct the force field properly. In my case, peptid + cnt + water molecules, what is your suggestion? Please guide me and explain more. How to do MD simulation of my system by gromacs? You have missing parameters in the .top/.itp file. You have those parameters already in ffbonded.itp for the CNT. As long as those parameters are compatible with the peptide force field (CHARMM27), then you just need to add those parameters. Again, that may be as simple as adding #include "cntffbonded.itp" of whatever it is to the .top file after the #include statement for the parent force field. Your only problem was #including another force field that re-defined a [defaults] directive. That is syntactically illegal. Nothing else was inherently problematic, unless you're mixing incompatible force fields, but I haven't seen any evidence of that. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
[gmx-users] Invalid order for directive defaults
Dear Justin Thanks for your reply. > In your previous setup, you were effectively trying to use CHARMM27 + some > other > force field related to the CNT. You can't do that. Thus, Gromacs is not appropriate for systems containing cnt. Is my deduction true? In my case, peptid + cnt + water molecules, what is your suggestion? Please guide me and explain more. How to do MD simulation of my system by gromacs? Any help will highly appreciated. -- gmx-users mailing listgmx-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
Re: [gmx-users] Invalid order for directive defaults
On 11/13/13 5:51 AM, Atila Petrosian wrote: Dear Justin Very thanks for your reply. I created a new topol.top file as below: 1) I used once default directive. 2) I put cnt.itp file in working directory. 3) I copied pr.top and renamed it to topol.top. I added #include "cnt.itp" in the end of topol.top file. I modified [ molecules ] directive. -- begining of topol.top file is as follows: ; Include forcefield parameters #include "charmm27.ff/forcefield.itp" [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] . . . . end of com.top file is as follows: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif #include "cnt.itp" ; Include water topology #include "charmm27.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "charmm27.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 CNT 1 SOL 1388 --- Previous error (Invalid order for directive defaults) was solved, but When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I encountered with this error: ERROR1 [file cnt.itp, line 2861]: No default Angle types . . . . . . ERROR 1218 [file cnt.itp, line 4078]: No default Angle types Fatal error: There were 1218 errors in input file(s). Lines 2861-4078 are related to [ angles ] directive in cnt.itp file. How to solve this issue? In your previous setup, you were effectively trying to use CHARMM27 + some other force field related to the CNT. You can't do that. What you can do (and need to do) is incorporate the nonbonded and bonded parameters related to the CNT into the parent force field. You may be able to simply #include the ffnonbonded.itp and ffbonded.itp files in the topology. Your current approach has simply deleted necessary information. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
[gmx-users] Invalid order for directive defaults
Dear Justin My cnt is infinite. I obtained cnt.top by g_x2top and then modified cnt.top to cnt.itp. For obtaining cnt.top, I used following files: --- ffcnt.atp: CA 12.01100 ; aromatic C --- ffcnt.n2t: CCA0.0012.011 3C 0.141 C 0.141 C 0.141 CCA0.0012.011 2C 0.141 C 0.141 --- ffcntbon.itp: [ bondtypes ] ; i j funcb0 kb CA CA 3 0.1418 47890.0 21.867 [ angletypes ] ; i j k functh0 cth ub0 cub CA CA CA 2 120.00 562.20 [ dihedraltypes ] ; i j k l funcphi0cp mult CA CA CA CA 5 0.00 25.12 0.00 0.00 --- ffcntnonbon.itp: [ atomtypes ] ;name at.num masscharge ptype sigma epsi CA 6 12.011000.00A 0.385 0.4396 --- In cnt.itp file, angle section of file is as follows: [ angles ] ; aiajak functc0c1c2c3 2 1 8 1 2 1 287 1 8 1 287 1 1 2 3 1 1 210 1 3 210 1 2 3 289 1 2 3 406 1 289 3 406 1 5 417 1 5 4 320 1 17 4 320 1 4 5 6 1 . . . . . . I saw system.gro file by VMD, there are all angles defined above in [angle] directive. -- gmx-users mailing listgmx-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
[gmx-users] Invalid order for directive defaults
Dear Justin Very thanks for your reply. I created a new topol.top file as below: 1) I used once default directive. 2) I put cnt.itp file in working directory. 3) I copied pr.top and renamed it to topol.top. I added #include "cnt.itp" in the end of topol.top file. I modified [ molecules ] directive. -- begining of topol.top file is as follows: ; Include forcefield parameters #include "charmm27.ff/forcefield.itp" [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] . . . . end of com.top file is as follows: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif #include "cnt.itp" ; Include water topology #include "charmm27.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "charmm27.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 CNT 1 SOL 1388 --- Previous error (Invalid order for directive defaults) was solved, but When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I encountered with this error: ERROR1 [file cnt.itp, line 2861]: No default Angle types . . . . . . ERROR 1218 [file cnt.itp, line 4078]: No default Angle types Fatal error: There were 1218 errors in input file(s). Lines 2861-4078 are related to [ angles ] directive in cnt.itp file. How to solve this issue? Any help will highly appreciated. -- gmx-users mailing listgmx-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
Re: [gmx-users] Invalid order for directive defaults
On 11/12/13 10:07 AM, Atila Petrosian wrote: 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 fcxfcyfcz 11 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 fcxfcyfcz 11 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 ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 #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 ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 #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
[gmx-users] Invalid order for directive defaults
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 fcxfcyfcz 11 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 fcxfcyfcz 11 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 ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 #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 ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 #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?
Re: [gmx-users] Invalid order for directive defaults
Fatal error: Invalid order for directive defaults, file ""/panfs/storage.local/scs/home/myunggi/gromacs-openmpi/share/gromacs/top/ffgmx.itp"", line 4 I think I have only one [ defaults ] section. Does Anybody have an idea? What is wrong? Check out http://wiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Invalid order for directive defaults
Dear gromca users, I'm a new user of gromacs. I'm trying to run energy minimization on the system of a short peptide and a lipid bilayer. The following is my top file. ; #include "ffgmx.itp" #include "../lipid.popc.itp" #include "popc.itp" #include "pro.itp" #include "ions.itp" #include "spc.itp" [ system ] ; name Fusion peptide on POPC [ molecules ] ; name number Protein 1 POPC128 Na 2 SOL 3655 +++ And I copied em.mdp with a little modification from the tutorial. +++ ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = cpp define = -DPOSRES constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no ++ After runing grompp I've got the following error message. ++ Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive defaults, file ""/panfs/storage.local/scs/home/myunggi/gromacs-openmpi/share/gromacs/top/ffgmx.itp"", line 4 I think I have only one [ defaults ] section. Does Anybody have an idea? What is wrong? Have a great day. -- Best wishes, MYUNGGI YI == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
