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

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

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

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

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