[gmx-users] OPLS-AA forcefield

2010-05-27 Thread you zou
Hi everyone, I have one simple question. I don't know is there any different between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these are different but when I use pdb2gmx tool there is no OPLS-AA forcefield to choose. Thank you

Re: [gmx-users] OPLS-AA forcefield

2010-05-27 Thread Justin A. Lemkul
you zou wrote: Hi everyone, I have one simple question. I don't know is there any different between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these are different but when I use pdb2gmx tool there is no OPLS-AA forcefield to choose. There is no difference. The presence of /L

Re: [gmx-users] OPLS-AA forcefield

2010-05-27 Thread Erik Marklund
Justin A. Lemkul skrev: you zou wrote: Hi everyone, I have one simple question. I don't know is there any different between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these are different but when I use pdb2gmx tool there is no OPLS-AA forcefield to choose. There is no

Re: [gmx-users] OPLS-AA forcefield

2010-05-27 Thread Justin A. Lemkul
Erik Marklund wrote: Justin A. Lemkul skrev: you zou wrote: Hi everyone, I have one simple question. I don't know is there any different between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these are different but when I use pdb2gmx tool there is no OPLS-AA forcefield to

[gmx-users] OPLS-AA forcefield parameters

2009-04-04 Thread Jacob Harvey
Dear All, I am trying to use the OPLS-AA force field to model some imidazole containing compounds. I've noticed that imidazole units are referenced in the ffoplsaa.atp file as the following: opls_557 14.00670 ; N1 in imidazole opls_558 12.01100 ; C2 in imidazole opls_559 14.00670 ;

Re: [gmx-users] OPLS-AA forcefield parameters

2009-04-04 Thread Justin A. Lemkul
Jacob Harvey wrote: Dear All, I am trying to use the OPLS-AA force field to model some imidazole containing compounds. I've noticed that imidazole units are referenced in the ffoplsaa.atp file as the following: opls_557 14.00670 ; N1 in imidazole opls_558 12.01100 ; C2 in

Re: [gmx-users] OPLS-AA forcefield parameters

2009-04-04 Thread Jacob Harvey
Thank you for your help Justin. I have corrected my naming problem in the pdb file. However, I am still getting errors. It does not seem to recognize the residues. BUT I dont actually have residues in my system, because I am not modeling a protein. So I am not sure what to put in the residue name

Re: [gmx-users] OPLS-AA forcefield parameters

2009-04-04 Thread Justin A. Lemkul
Jacob Harvey wrote: Thank you for your help Justin. I have corrected my naming problem in the pdb file. However, I am still getting errors. It does not seem to recognize the residues. BUT I dont actually have residues in my system, because I am not modeling a protein. So I am not sure what

Re: [gmx-users] OPLS-AA forcefield parameters

2009-04-04 Thread Justin A. Lemkul
Jacob Harvey wrote: Justin, How do I go about running topolgen on a linux system? There doesn't seem to be instructions for use, but I'm not familiar with perl scripts. Also I'd just like to say thank you for all your help. You've been really good with responding to my e-mail. I know that