Re: [gmx-users] decimal charge instead of integer

2010-01-21 Thread Justin A. Lemkul
Carla Jamous wrote: Hi, In order to run my simulation, I had to insert GDP parameters in ffamber94 (the force field I'm using). However, I'm having a problem with GDP charge. the charge of every charge group in top file should be an integer. But I'm getting a decimal charge which gives me

Re: [gmx-users] decimal charge instead of integer

2010-01-21 Thread David van der Spoel
On 1/21/10 2:12 PM, Carla Jamous wrote: Hi, In order to run my simulation, I had to insert GDP parameters in ffamber94 (the force field I'm using). However, I'm having a problem with GDP charge. the charge of every charge group in top file should be an integer. But I'm getting a decimal charge

Re: [gmx-users] decimal charge instead of integer

2010-01-21 Thread Erik Marklund
Carla Jamous skrev: Hi, In order to run my simulation, I had to insert GDP parameters in ffamber94 (the force field I'm using). However, I'm having a problem with GDP charge. the charge of every charge group in top file should be an integer. But I'm getting a decimal charge which gives me

Re: [gmx-users] decimal charge instead of integer

2010-01-21 Thread Erik Marklund
Carla Jamous skrev: Thank you Justin, but I ran a simulation before this one with GTP it worked fine. GDP GTP parameters are identical except for GDP having less atoms. This is why I can't understand why I don't get an integer charge while I did in my previous simulation. Carla Well, if

Re: [gmx-users] decimal charge instead of integer

2010-01-21 Thread Justin A. Lemkul
Carla Jamous wrote: Thank you Justin, but I ran a simulation before this one with GTP it worked fine. GDP GTP parameters are identical except for GDP having less atoms. This is why I can't understand why I don't get an integer charge while I did in my previous simulation. OK, but this

Re: [gmx-users] decimal charge instead of integer

2010-01-21 Thread Thomas Piggot
If using an amber forcefield and GTP/GDP you can use the parameters on the following website. I have used the ATP/ADP ones and have had no problems with many different systems and ATP/ADP conformations with which I used to test these parameters.

Re: [gmx-users] decimal charge instead of integer

2010-01-21 Thread Carla Jamous
Thanks everyone, you were right, it doesn't work if I only take off one phosphate from GTP. I was using the wrong parameters, now I have an integer total charge. Carla On Thu, Jan 21, 2010 at 2:36 PM, Thomas Piggot t.pig...@bristol.ac.ukwrote: If using an amber forcefield and GTP/GDP you can

Re: [gmx-users] decimal charge instead of integer

2010-01-21 Thread Chandan Choudhury
Hi Tom !!! Can you guide to incorporate the AMBER parameter for ATP ( http://www.pharmacy.manchester.ac.uk/bryce/amber#cof) in ffamber. I am using ffamber for the simulation of Protein + ATP. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Jan 21, 2010 at 7:06 PM, Thomas Piggot