[gmx-users] validation of ligand parametrization

2011-01-26 Thread mohsen ramezanpour
Dear All and specially Dear Dr.Justin I generated parameters for a typical ligand. now I want to validate it. How can I do it? Please let me know references for doing this. Of course I have read the article by Dr.Justin(Alzeimer),Unfortunately I couldn't understand it completely and very good. Is

Re: [gmx-users] validation of ligand parametrization

2011-01-26 Thread Justin A. Lemkul
mohsen ramezanpour wrote: Dear All and specially Dear Dr.Justin I generated parameters for a typical ligand. now I want to validate it. How can I do it? Please let me know references for doing this. Of course I have read the article by Dr.Justin(Alzeimer),Unfortunately I couldn't understand

Re: [gmx-users] validation of ligand parametrization

2011-01-26 Thread mohsen ramezanpour
Dear Justin I don't want to rely on PRODRG server as others. I want to do my work as accurate as possible. Absolutely I read your papar and I know PRODRG present bad results for estimating free energies. I want to parametrize my drugs by GROMOS43A1 parameters as you said. I know completely how to

Re: [gmx-users] validation of ligand parametrization

2011-01-26 Thread Mark Abraham
On 26/01/2011 11:10 PM, mohsen ramezanpour wrote: Dear Justin I don't want to rely on PRODRG server as others. I want to do my work as accurate as possible. Absolutely I read your papar and I know PRODRG present bad results for estimating free energies. I want to parametrize my drugs by

Re: [gmx-users] validation of ligand parametrization

2011-01-26 Thread mohsen ramezanpour
Dear Dr Mark Thanks for your guidances. I am sorry for my last question.My english is not very good,I hope I could say what was in my mind not what you read :-) by the way,Thanks for your attention and your reply. On Wed, Jan 26, 2011 at 3:55 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On