[gmx-users] Invalid order for directive atomtypes

Dear GMX users, To generate a topology file for an arbitrary molecule (TP) on graphite surface, I used g_x2top program to generate “TP.itp” file and I manually construct graphite.itp file. Generated topology file is as the following: #include ./oplsaa.ff/forcefield.itp #include TP.itp

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

On 8/23/13 3:29 AM, afsaneh maleki wrote: Dear GMX users, To generate a topology file for an arbitrary molecule (TP) on graphite surface, I used g_x2top program to generate “TP.itp” file and I manually construct graphite.itp file. Generated topology file is as the following: #include

[gmx-users] Invalid order for directive atomtypes

PDB file used :http://www.rcsb.org/pdb/explore.do?structureId=1cx2 Commands used: http://pastebin.com/raw.php?i=YYG5ad7A Compressed folder containing all files (10.2 MB): http://www.sendspace.com/file/rka8ei So I want to simulate this complex. I am having problems with the .itp's and do not know

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

Hi Jonathan, The itp's for the ligands were given atomtype sections, but atomtypes (and other *types) may only be defined before any moleculetype definition (check chapter 5 of the manual for the topology format). You'll need to remove anything before the moleculetype directive from the itp files

[gmx-users] Invalid order for directive atomtypes

Hello Users, I am a final year project student.I am doing simulation of gangliosdie gm1 using gromacs 4.5.4. I am encountering an error in the energy minimisation step(grompp -f ions.mdp -c gm1_solv.gro -p gm12.top -o ions.tpr) saying * ---

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

On 3/05/2011 7:13 PM, Geethu Issac wrote: Hello Users, I am a final year project student.I am doing simulation of gangliosdie gm1 using gromacs 4.5.4. I am encountering an error in the energy minimisation step(grompp -f ions.mdp -c gm1_solv.gro -p gm12.top -o ions.tpr) saying *

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

Geethu Issac wrote: Hello Mark. yes i did check the link :) . but the error has been shown in the ffgmxnb.itp file.I had received the itp file from sega and i modified it to a topology file. Then either the original file was somehow incorrect, whatever you did to it is incorrect, or

[gmx-users] Invalid order for directive atomtypes

Thanks Mark.I will check with the format specified and am really sorry for the inconvenience. -- *Geethu Issac* * A life spent making mistakes is not only more honorable, but more useful than a life spent doing nothing. -George Bernard Shaw* -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Invalid order for directive atomtypes

hello friends, I am doing simulation of ganglioside gm2 and am getting the following error. Fatal error: Syntax error - File gm2gang.top, line 6 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Can anyone please help me in this.I am new to gromacs. -- *Geethu Issac* * A

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

On 5/04/2011 4:59 PM, Geethu Issac wrote: hello friends, I am doing simulation of ganglioside gm2 and am getting the following error. Fatal error: Syntax error - File gm2gang.top, line 6 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Can anyone please help me in