[gmx-users] Re: Adding small molecule parameters to charmm force field

I have obtained the force field paramter of a small molecule (parameterized for CHARMM FF) and now I want to ad this to the charmm force field so that i can use it for simulation . I searched gmx userlist but didn't find any appropriate thread.. can anybody let me know ?? -- Bharat Ph.D. Candidat

[gmx-users] Re: RE: simulation of a metal binding sites (bharat gupta)

Hi, If you know the structure of the zinc binding domain and assume that the zinc ion stays in place it may be all right to use the bonded representation. Recent publications: @article{Lin2010, author = {Lin, F and Wang, R}, title = {Systematic Derivation of {AMBER} Force Field Parameters Appl

[gmx-users] where to insert a new include DPOSRES in topology file?

Dear all, I would like to do a position restraint MD by applying position restraints not only to my protein but also to its ligand. In order to do it, I created with genrestr a new protligposre.itp file in which I indicated the group to be restrained as Protein_lig. In this protligposre.itp file, t

Re: [gmx-users] where to insert a new include DPOSRES in topology file?

Anna Marabotti wrote: Dear all, I would like to do a position restraint MD by applying position restraints not only to my protein but also to its ligand. In order to do it, I created with genrestr a new protligposre.itp file in which I indicated the group to be restrained as Protein_lig. In

[gmx-users] Fwd: Adding small molecule parameters to charmm force field

Hi, I have obtained the force field paramter of a small molecule (parameterized for CHARMM FF) and now I want to ad this to the charmm force field so that i can use it for simulation . I searched gmx userlist but didn't find any appropriate thread.. can anybody let me know ?? -- Bharat Ph.D. Cand

Re: [gmx-users] Fwd: Adding small molecule parameters to charmm force field

bharat gupta wrote: Hi, I have obtained the force field paramter of a small molecule (parameterized for CHARMM FF) and now I want to ad this to the charmm force field so that i can use it for simulation . I searched gmx userlist but didn't find any appropriate thread.. can anybody let me k

Re: [gmx-users] Fwd: Adding small molecule parameters to charmm force field

Thanks for the information .. I have got the topology file + .inp file of the molecule .. On Fri, Feb 18, 2011 at 4:45 AM, Justin A. Lemkul wrote: > > > bharat gupta wrote: > >> Hi, >> >> I have obtained the force field paramter of a small molecule >> (parameterized for CHARMM FF) and now I want

[gmx-users] Target implementation date for gb_saltconc?

Dear GROMACS developers and users, Our research group is interested in performing GBSA simulations with GROMACS, but we would need to perform them with a nonzero salt concentration. I was wondering if there are plans to implement the gb_saltconc parameter, and if so, when it might become availabl

Re: [gmx-users] WHAM with multiple force constants

On 2/10/11 Feb 10,6:08 AM, jk...@ifr88.cnrs-mrs.fr wrote: Hi, I'm running an Umbrella Sampling analysis, with 1A steps in the reaction coordinate (distance) to estimate a PMF. However, owing to (high?) energetic barriers between my two proteins, some coordinates are not sampled. I intend to r

[gmx-users] configure: error: cannot compute sizeof (off_t)

Dear experts, I have installed Gromacs under the normal configuration and am now attempting to install the mpi version of mdrun on a machine, however I am getting this error during the configuration: configure: error: cannot compute sizeof (off_t) See `config.log' for more details. I cant seem t

Re: [gmx-users] configure: error: cannot compute sizeof (off_t)

On 19/02/2011 2:32 PM, Justin Kat wrote: Dear experts, I have installed Gromacs under the normal configuration and am now attempting to install the mpi version of mdrun on a machine, however I am getting this error during the configuration: configure: error: cannot compute sizeof (off_t) See

Re: [gmx-users] about -CN triple bond

Hi, I have tried to add [ position restraints ] 2 1 1000 1000 1000 ; Restrain to a point 1 1 1000 0 1000 ; Restrain to a line (Y-axis) 3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane) in the end of the topology file. In the em. process, I get the eroor msg. Fatal error: Invalid dihedral type 100

Re: [gmx-users] about -CN triple bond

On 19/02/2011 3:02 PM, C.Y. Chang wrote: Hi, I have tried to add [ position restraints ] This is misspelled. Surely grompp warned about this? 2 1 1000 1000 1000 ; Restrain to a point 1 1 1000 0 1000 ; Restrain to a line (Y-axis) 3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane) in the end of

Re: [gmx-users] about -CN triple bond

Hi, The errpr msg. that I expressed in the previous mail is unclear. It really happened in the grompp step of my dealinw with the em. The manual shows that the viste can be used by [ virtual sites2 ] ; Site from funct a 5 1 2 1 0.7439756 What should I choose the vsite for the -CN group? (2, 3fd

Re: [gmx-users] about -CN triple bond

On 19/02/2011 5:18 PM, C.Y. Chang wrote: Hi, The errpr msg. that I expressed in the previous mail is unclear. It really happened in the grompp step of my dealinw with the em. The manual shows that the viste can be used by [ virtual sites2 ] That's misspelled too. Underscores are significant.