Re: Re: [gmx-users] Nose-hoover T-coupling in REMD

Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, January 10, 2011. For all questions about CloudBroker, please contact the compan

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010/12/26 ms > On 25/12/10 02:12, Qin Qiao wrote: >>> >>> Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me?

[gmx-users] Atomype HW not found

Dear all, I have "Atomype HW not found" error when I use gromos43a1 in water at the end of grompp. However there is no error if I just change the forcefield to oplsaa. My topology file follows. Any suggestions? trevor ; Include forcefield parameters #include "gromos43a1.ff/forcefield.itp" [ mol

Re: [gmx-users] To make continuous trj in REMD

2011/1/7 Justin A. Lemkul > > > Qin Qiao wrote: >> >> >> 2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >>    Qin Qiao wrote: >> >> >> >>        2011/1/7 Justin A. Lemkul >         >        >> >> >> >> >> >>    

[gmx-users] Atomtpe HW not found-2

Dear friends, My run commands are below. It works without any error. However if I add -water tip3p at the end of pdg2gmx ... line it causes an error (Atomtpe HW not found) at grompp time. Could anyone explain the difference? trevor pdb2gmx -ignh -f XXX.pdb -o fws.gro -p fws.top editconf -f fws.g

Re: [gmx-users] Atomtpe HW not found-2

On 10/01/2011 2:41 AM, trevor brown wrote: Dear friends, My run commands are below. It works without any error. However if I add -water tip3p at the end of pdg2gmx ... line it causes an error (Atomtpe HW not found) at grompp time. Could anyone explain the difference? trevor pdb2gmx -ignh -f XXX

[gmx-users] Pioglitazone Tautomers

Hi All, I am performing molecular docking and molecular dynamics simulations of the thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous different tautomeric states; I have attached a figure depicting several of

Re: [gmx-users] Pioglitazone Tautomers

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RE: [gmx-users] Pioglitazone Tautomers

If you have the pKa for each of those three groups, then you can calculate that yourself very quickly. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu

Re: [gmx-users] Pioglitazone Tautomers

On 10/01/2011 10:11 AM, Nancy wrote: Hi All, I am performing molecular docking and molecular dynamics simulations of the thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous different tautomeric states; I h

[gmx-users] Water models usage info

Dear Mark, Thank you for your reply which solved my problem. I want to add something for all gmx-users. I looked at the force field folders in share/top in which possible usable water models for each force field are listed in watermodels.dat files. If you want to use a different model that is not i

Re: [gmx-users] Pioglitazone Tautomers

Hi Nancy, This isn't really a Gromacs related question, and it would be better fit on some chemistry forum. Anyway, whatever answer may come to you, mind that you're interested in the receptor bound form, which may not be what you'll find to be the dominant form. It will depend on the hydrogen bon