[gmx-users] ATP/ADP+Pi

2012-10-26 Thread ????????
GMX-users: I am working with ATP+protein and ADP+Pi+protein in gromos43a1.ff force field,but I find only ATP parameters in the aminoacids.rtp file .Where can I achieve the ADP+Pi parameters ??? I wanted use the parameters from((http://www.pharmacy.manchester.ac.uk/bryce/amber) )

Re: [gmx-users] ATP/ADP+Pi

2012-10-26 Thread Justin Lemkul
On 10/26/12 11:12 AM, 闪耀星空 wrote: GMX-users: I am working with ATP+protein and ADP+Pi+protein in gromos43a1.ff force field,but I find only ATP parameters in the aminoacids.rtp file .Where can I achieve the ADP+Pi parameters ??? I wanted use the parameters

Re: [gmx-users] ATP/ADP+Pi

2012-10-26 Thread João M . Damas
Hello, At our group we have parameterized ATP, ADP and Pi to use with ABC transporters. Paper with the parameterization: http://dx.doi.org/10.1021/jp905735y Papers using the parameterized molecules: http://dx.doi.org/10.1002/prot.23023 http://dx.doi.org/10.1002/pro.650

[gmx-users] Holes in the solvent!

2012-10-26 Thread Arman M. Soufiani
Dear Gromacs users, I am simulating a protein on a polymer surface for further adsorption free energy calculation. However, after performing the NVT run either for short or long durations I found out that couple of holes appear in the physiological saline solution (solvent)!!! Additionally, even

Re: [gmx-users] Freeze group atoms changing position

2012-10-26 Thread Alex Marshall
Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip. Bogdan: I don't think I'm using constraints other than freeze groups. I wasn't using energy group exclusions though. I tried running the simulation from the same initial configuration with

[gmx-users] calculate RDC from MD trajectory

2012-10-26 Thread Gurunath Katagi
Dear all, I want to compare the RDC data from MD simulation of a protein with those derived from RDC. I was wondering whether there is any program or implementation for calculation of RDC in gromacs.. There have been studies which have computed RDC from md simulation trajectories, for example, .

Re: [gmx-users] Holes in the solvent!

2012-10-26 Thread Justin Lemkul
On 10/26/12 3:25 PM, Arman M. Soufiani wrote: Dear Gromacs users, I am simulating a protein on a polymer surface for further adsorption free energy calculation. However, after performing the NVT run either for short or long durations I found out that couple of holes appear in the

[gmx-users] Conceptual question about the representation of dihedral angles in Gromacs

2012-10-26 Thread Andrew DeYoung
Hi, If you have time, may I ask a conceptual question about how dihedral angles are specified in force fields? Consider ethane, a two-carbon hydrocarbon (H_3C-CH_3). It has two carbon atoms and six hydrogen atoms. Call the carbons C1 and C2. Hydrogens H1, H2, and H3 are bonded to C1.

回复： [gmx-users] ATP/ADP+Pi

2012-10-26 Thread 闪耀星空
Thanks for your help!! About these paper,I have just read them. In your paper,you selected 43a1 force field directly and did not talk about ATP/ADP+Pi parameters.But in my 43a1 force field ,the ATP parameters are exist,ADP and Pi are not.I use gromacs 4.5.5 versions. WHY?? Thanks!!

回复： 回复： [gmx-users] ATP/ADP+Pi

2012-10-26 Thread 闪耀星空
Hello How to parameterize ATP, ADP and Pi ?my initiating structure has it,but the force field has not define the ATP,ADP,Pi and not recognition it .thanks -- 原始邮件 -- 发件人: 闪耀星空382209...@qq.com; 发送时间: 2012年10月27日(星期六) 中午11:03 收件人: Discussion list for