[gmx-users] Ligand charge issues

Hi Gromacs users, I am studying the protein-ligand interaction using amber99sb-ILDN force field in gromacs 4.6.2. To create the ligand topology (lipid A), I have used online version of ACPYPE/antechamber.http://webapps.ccpn.ac.uk/acpype/ I have read a lot more time that charge on different atoms

Re: [gmx-users] Ligand charge issues

In https://code.google.com/p/acpype/ you can look the wikis and you see the explanations about the partial charges. The best solution, though not straightforward, would be using http://q4md-forcefieldtools.org/REDS/ Alan On 2 September 2013 11:27, Muhammad Ayaz Anwar wrote: > Hi Gromacs user

[gmx-users] adding ETHANOL to CGennFF in gromacs has problem

Hello, I am trying to add ethanol as a new residue to CGenFF force field in gromacs. Basically, I need to bring this information from charmm rtf file to the gromacs format. This is the information taken from rtf file of charmm. RESI ETOH          0.00 ! C2H6O Ethanol, adm jr. GROUP ATOM C1   CG

Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem

On 9/2/13 12:59 PM, Golshan Hejazi wrote: Hello, I am trying to add ethanol as a new residue to CGenFF force field in gromacs. Basically, I need to bring this information from charmm rtf file to the gromacs format. This is the information taken from rtf file of charmm. RESI ETOH 0.

Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem

Please make sure to keep the discussion on the mailing list. On 9/2/13 1:27 PM, Golshan Hejazi wrote: This is the gro file that I am using: ETHANOL 9 1ETHAC11 3.133 3.266 0.008 1ETHAO12 3.244 3.350 -0.021 1ETHA HO13 3.324 3.296 -0.015

Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem

Thanks Justin for looking at the files. I am using the gro and top file to generate a tpr with the following mdp file in order to see if everything is all right: title                    = geometry-optimization cpp                      = /usr/bin/cpp include                  = integrator        

Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem

On 9/2/13 2:02 PM, Golshan Hejazi wrote: Thanks Justin for looking at the files. I am using the gro and top file to generate a tpr with the following mdp file in order to see if everything is all right: title= geometry-optimization cpp = /usr/bin/cpp

Re: [gmx-users] Distance restraints exploding system

Have you tried with even less restraints? I found systems are not always stable with more than the bare minimum of restraints On Sun, Sep 1, 2013 at 7:54 PM, Trayder Thomas wrote: > It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have > an impact. I've tried being gentle,

Re: [gmx-users] Long range Lennard Jones

On Thu, Aug 29, 2013 at 7:18 AM, Gianluca Interlandi wrote: > Justin, > > I respect your opinion on this. However, in the paper indicated below by BR > Brooks they used a cutoff of 10 A on LJ when testing IPS in CHARMM: > > Title: Pressure-based long-range correction for Lennard-Jones interactions

[gmx-users] Re: MD vs. free energy simulations

Dear Justin, I set the couple_intramol parameter to yes and rerun the free energy simulations. mdrun was able to fully utilize all the cores in the system but there's one issue. The free energy of solvation is vastly different if the parameter is set to 'no' (DG=-408.10 +/- 8.69 kJ/mol) or 'yes'

Re: [gmx-users] Re: MD vs. free energy simulations

On 9/2/13 9:43 PM, Jernej Zidar wrote: Dear Justin, I set the couple_intramol parameter to yes and rerun the free energy simulations. mdrun was able to fully utilize all the cores in the system but there's one issue. The free energy of solvation is vastly different if the parameter is set to