Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

f. You won't be able to properly describe the transition state > using classical means only. > > Cheers, > > Tsjerk > > On Thu, Feb 19, 2009 at 1:19 PM, Justin A. Lemkul wrote: > > > > > > Ji Liu wrote: > >> > >> Hi Tsjerk, > &

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

post to the user list and see if any of us > has already been there... > > Cheers, > > Tsjerk > > > On Thu, Feb 19, 2009 at 10:35 AM, Ji Liu wrote: > > Hi Tsjerk, > > > > Thanks a lot. > > Surely I can't modify the force field by my self. It

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Hi Tsjerk, Thanks a lot. Surely I can't modify the force field by my self. It's impossible to me to understand all of things you mentioned. So is it the only way to achieve my purpose? If so, it's so frustrating. I've been trying my best to contact with the author of one of my references. He appli

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

gestion? Thank again. JI On Thu, Feb 19, 2009 at 2:45 PM, Mark Abraham wrote: > Ji Liu wrote: > >> Hello everyone, >> >> I'm gonna run MD simulation with a enzyme/substrate system. Here the >> substrate must connected with the side chain of an activity residue of

[gmx-users] Problem in preparation of the enzyme/substrate complex

Hello everyone, I'm gonna run MD simulation with a enzyme/substrate system. Here the substrate must connected with the side chain of an activity residue of enzyme through covalent bond. However, i really have no idea about the preparation of such a complex structure file. Actually, i tried to modi