[gmx-users] FEP for ligand mutation

2012-01-22 Thread Sanku M
Hi,   Is it possible in GROMACS4.5 to perform computation of relative binding free energy of a ligand to a protein due to mutation in the ligand ( or due tio mutation in the protein)?  I have done the computation of solvation free energy of a solute in a solvent using FEP but looking for some

[gmx-users] Implicit solvent model in Gromacs

2012-01-22 Thread Gianluca Interlandi
Dear gromacs users list, I noticed that gromacs can perform simulations with an implicit solvent model using a GBSA method. Is it compatible with the CHARMM22 force field? Thanks, Gianluca - Gianluca Interlandi, PhD

Re: [gmx-users] Implicit solvent model in Gromacs

2012-01-22 Thread Mark Abraham
On 23/01/2012 1:01 PM, Gianluca Interlandi wrote: Dear gromacs users list, I noticed that gromacs can perform simulations with an implicit solvent model using a GBSA method. Is it compatible with the CHARMM22 force field? Thanks, Gianluca

[gmx-users] problem in creating forcefield.doc

2012-01-22 Thread Anushree Tripathi
*I am using gromacs 4.5.3 version and I am trying to follow the tutorials. For ** starting I am following the *KALP15 in DPPC* ** tutorial(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html). *I am not getting the point that is given below :

[gmx-users] Regarding Extracting Coordinates of Solvent in FCS alone

2012-01-22 Thread Ravi Kumar Venkatraman
Dear All, I have situation rite now like, I have to take the Solute and Solvent Coordinates from First Coordination Shell / FCS + Second CS. Please give me some suggestion for doing the same. Thank you *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA.

Re: [gmx-users] problem in creating forcefield.doc

2012-01-22 Thread Mark Abraham
On 23/01/2012 5:13 PM, Anushree Tripathi wrote: /I am using gromacs 4.5.3 version and I am trying to follow the tutorials. For // starting I am following the *KALP15 in DPPC* // tutorial(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html).

Re: [gmx-users] Regarding Extracting Coordinates of Solvent in FCS alone

2012-01-22 Thread Mark Abraham
On 23/01/2012 5:19 PM, Ravi Kumar Venkatraman wrote: Dear All, I have situation rite now like, I have to take the Solute and Solvent Coordinates from First Coordination Shell / FCS + Second CS. Please give me some suggestion for doing the same. Have a think about what geometric

Re: [gmx-users] FEP for ligand mutation

2012-01-22 Thread Mark Abraham
On 23/01/2012 7:06 AM, Sanku M wrote: Hi, Is it possible in GROMACS4.5 to perform computation of relative binding free energy of a ligand to a protein due to mutation in the ligand ( or due tio mutation in the protein)? I have done the computation of solvation free energy of a solute in a

Re: [gmx-users] unfold the coordinates

2012-01-22 Thread Mark Abraham
On 22/01/2012 6:02 PM, Chandan Choudhury wrote: Hi gmx-users !! How does the gromacs unfolds the coordinates of the atoms when the simulation is run using -pbc xyz ? I do not know what you mean by unfold. If a particle in subsequent time crosses the boundary say x / y or both axis , then

[gmx-users] Gromacs and CHARMM silicate force field

2012-01-22 Thread Gianluca Interlandi
I would like to ask whether it is possible to use in Gromacs the CHARMM parameters for silicates. More generally, is it easy to convert CHARMM parameter and topology files to the gromacs format? Thanks, Gianluca - Gianluca Interlandi,

Re: [gmx-users] problem in creating forcefield.doc

2012-01-22 Thread Anushree Tripathi
I have created one file named it as forcefield.doc and paste the contents of forcefield.itp into it and also include lipid.itp file.The content of my forcefield.doc file is given below: #define _FF_GROMOS96 #define _FF_GROMOS53A6 [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJ