Re: [gmx-users] regarding dimethylated lysine topology file

I thing the the function is not written well... It is: Vd=k_phi(1+cos(n*phi-phi_eq)) Antonia >prasun kumar said: > --000e0cd20d869ab935046434ec49 > Content-Type: text/plain; charset=ISO-8859-1 > Content-Transfer-Encoding: 7bit > > Respected all > I drew the structure using the drawing tool

Re: [gmx-users] regarding dimethylated lysine topology file

Hi, the function used by GROMACS is Vd (öijkl ) = kö (1 + cos(nö − ös )), for proper dihedrals (periodic type). Take a look at Chapter 4, of GROMACS-4-0 manual. Antonia >prasun kumar said: > --000e0cd20d869ab935046434ec49 > Content-Type: text/plain; charset=ISO-8859-1 > Content-Transfer-Enc

Re: [gmx-users] regarding dimethylated lysine topology file

prasun kumar wrote: Respected all I drew the structure using the drawing tool available in PRODRG server then I went for topology file generation,but the server is deleting almost all the hydrogen atoms while writing the topology file for gromacs can any one tell me why it is doing like this

[gmx-users] regarding dimethylated lysine topology file

Respected all I drew the structure using the drawing tool available in PRODRG server then I went for topology file generation,but the server is deleting almost all the hydrogen atoms while writing the topology file for gromacs can any one tell me why it is doing like this? another question I got

Re: [gmx-users] regarding dimethylated lysine topology file

prasun kumar wrote: respected all I m tryin to generate a topology file for dimethylated lysine using PRODRG server,but I found that its not working...can you plz help me in gettin some another servers or any method... Saying "its not working" is useless. If there is som

Re: [gmx-users] regarding dimethylated lysine topology file

Dear Prasun, I think you can get the help of Chem 3D for fixing this problem. First you have to generate the topology with Chem 3D then get the gromacs format with PRODRG server of the same. I hope it will help you, with regards anil On Mon, Mar 2, 2009 at 2:21 PM, prasun kumar wrote: > respe

[gmx-users] regarding dimethylated lysine topology file

respected all I m tryin to generate a topology file for dimethylated lysine using PRODRG server,but I found that its not working...can you plz help me in gettin some another servers or any method... is it possible to change gromacs topology file to charmm topology file thanx in ad