[gmx-users] Installing Extended Genbox

2013-09-30 Thread Tegar Nurwahyu Wijaya
Dear all, I want to install Extended Genbox from gerrit. https://gerrit.gromacs.org/#/c/1175/ How can I put this code into my existing gromacs installation? Thanks. Regards, Tegar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please s

Re: [gmx-users] ionomer topolgy

2013-09-30 Thread Ehsan Sadeghi
I was pretty confident that I am modifying the right file. apparently I did not access to the main file; so I asked my supervisor and he provided me with a proper access to the files. Thanks again Justin. - Original Message - From: "Justin Lemkul" To: "Discussion list for GROMACS users

Re: [gmx-users] ionomer topolgy

2013-09-30 Thread Ehsan Sadeghi
Many thanks Justin. Apparently I was modifying the .rtp file in the wrong location; now the pdb2gmx works and I can start the modelling. I also have some concern about my pdb file. i generated from my drawing in Avogadro, with some arbitrary bond length and angle. I hope that I can find the c

Re: [gmx-users] ionomer topolgy

2013-09-30 Thread Justin Lemkul
On 9/30/13 4:40 PM, Ehsan Sadeghi wrote: Many thanks Justin. Apparently I was modifying the .rtp file in the wrong location; now the pdb2gmx works and I can start the modelling. In the future, make sure you're providing accurate answers to the questions being asked. I asked about this at

[gmx-users] OPLS/AA + TIP5P, anybody?

2013-09-30 Thread Christopher Neale
One a system passes EM and a couple of ps of MD, is it always stable indefinitely? If not, then something is wrong somewhere. -- original message -- Dear Chris, I put one tip5p molecule in a center of dodecahedral box - 2nm from that molecule to walls, filled it with tip5p, ran 6000 steps of st

Re: [gmx-users] ionomer topolgy

2013-09-30 Thread Justin Lemkul
On 9/30/13 2:23 PM, Ehsan Sadeghi wrote: Yes, I have introduced the new .rtp entry in /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp. What could be wrong? The outcome defies logic. If the .rtp entry were in that file, pdb2gmx would not throw that error. Can you provide

Re: [gmx-users] ionomer topolgy

2013-09-30 Thread Ehsan Sadeghi
Yes, I have introduced the new .rtp entry in /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp. What could be wrong? - Original Message - From: "Justin Lemkul" To: "Discussion list for GROMACS users" Sent: Monday, September 30, 2013 11:16:57 AM Subject: Re: [gmx-users]

Re: [gmx-users] ionomer topolgy

2013-09-30 Thread Justin Lemkul
On 9/30/13 12:50 PM, Ehsan Sadeghi wrote: Thanks Justin, I modified the pdb file, but it cannot recognize my residue LIG. Here is the error: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading nafion5.pdb... Read 46 atoms Analyzing pdb file Spl

Re: [gmx-users] ionomer topolgy

2013-09-30 Thread Ehsan Sadeghi
Thanks Justin, I modified the pdb file, but it cannot recognize my residue LIG. Here is the error: Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading nafion5.pdb... Read 46 atoms Analyzing pdb file Splitting chemical chains based on TER records or

Re: [gmx-users] (no subject)

2013-09-30 Thread Justin Lemkul
On 9/30/13 5:19 AM, suhani nagpal wrote: Greetings I have a large protein of 303 residues and one of the lysine is acetylated in the same. The forcefield selection according to the options says as follows: Residue 'ALY' not found in residue topology database For more information and tips for

[gmx-users] (no subject)

2013-09-30 Thread suhani nagpal
Greetings I have a large protein of 303 residues and one of the lysine is acetylated in the same. The forcefield selection according to the options says as follows: Residue 'ALY' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS we