[gmx-users] How to calculate the free energy difference of solvation for a Tyr-Phe mutation!

article on the subject.  Thanks for any advice or comments on these not so specific questions - sry about that!Mikko Hellgren - Graduate Student[EMAIL PROTECTED] One cannot avoid making mistakes if one tries to produce a set of words, or of ma

[gmx-users] LIE energy calculation!

Hi Dear users, I have started to do calculations of the binding between a protein and different ligands. I have read articles on the LIE method and one tutorial. But still I have some quite general questions. I am using Cut-off and NVT ensamble. 1. When I run my ligands in a water solution without

[gmx-users] g_lie restraints, neutral ??

Hi MD people! Some questions about g_lie. My purpose is to score different ligands and get a rough estimation of the free energy of binding between free and bound state of the ligands and protein of interest. 1. When I run my ligands in water without the protein, should I add counterions (Cl

[gmx-users] Preformance on AMD X2!

me. Any comment or experience of this or should I consider Intel/Xeon/Opeteron instead. But take the tight budget in consideration when you ansewer to this. Many thanks for any comments Mikko Hellgren, PhD student at Karoliska Institutet

Re: [gmx-users] need suggestion for building TMA

Hi, I would consider to try to use the program genconf in Gromacs. With this program you can stack and multiply a given coordinate file "like a small child playing with wooden blocks" - Gromacs manual. Mikko Hellgren PhD student at Karolinska Institutet [EMAIL PROTECTED] Message: 3

[gmx-users] Request for PDB with the same label as in Gromocs topologies.

great full for any advice on that also. Best, Mikko Hellgren PhD student at Karolinska Institutet [EMAIL PROTECTED] <--- if you have the pdb I want, please send it to me... begin:vcard n:Hellgren;Mikko fn:Mikko Hellgren tel;cell:+46-737280550 tel;fax:+46-8-338453 tel;work:+46-8-52487

Re: [gmx-users] Request for PDB with the same label as in Gromocs topologies.

force fields at this point so you would be better off looking > elsewhere if you want to use OPLS. > > Incidentally, aside from getting force field parameters somewhere, you > may or may not need to also compute partial charges (I think in OPLS > partial charges are more or less link