Re: [gmx-users] Invalid order for directive defaults

2013-11-13 Thread Justin Lemkul
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 #i

[gmx-users] Invalid order for directive defaults

2013-11-13 Thread Atila Petrosian
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

Re: [gmx-users] Invalid order for directive defaults

2013-11-13 Thread Justin Lemkul
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

[gmx-users] Invalid order for directive defaults

2013-11-13 Thread Atila Petrosian
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 mole

Re: [gmx-users] Invalid order for directive defaults

2013-11-13 Thread Justin Lemkul
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 o

[gmx-users] Invalid order for directive defaults

2013-11-13 Thread Atila Petrosian
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 --

[gmx-users] Invalid order for directive defaults

2013-11-13 Thread Atila Petrosian
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 ] direc

Re: [gmx-users] Invalid order for directive defaults

2013-11-12 Thread Justin Lemkul
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 prot

[gmx-users] Invalid order for directive defaults

2013-11-12 Thread Atila Petrosian
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

Re: [gmx-users] Invalid order for directive defaults

2008-01-11 Thread Mark Abraham
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.

[gmx-users] Invalid order for directive defaults

2008-01-11 Thread Myunggi Yi
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.it