Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

Hi, You need to understand how AMBER uses the contents of the prm file, and how to produce suitable .rtp and atom type entries for use with GROMACS. This will mean some spending some quality time with the documentation. That's one reason that such simulations are not a good idea for someone

Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

Hi I have ff of heme fe---o2 some one use it before these are amber heme ff he use amber 99sb and this heme ff in his md simulation but he done his work in amber. Can you guide me that how I can use this heme ff of amber in combination with amber99sb at number 6 position in gromacs On Jun 14,

Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

Dear sir i have force field for O2 now some one work over it before its the .prm file he use to run simulation amber99 force field and use there own lab heme generated ff heme fe 02 now how i can use these amber heme force field in Gromacs thanks. On Fri, Jun 16, 2017 at 3:23 AM, Mark

Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

Hi, Generating a suitable model for such a system, plus its parameters, is a lot of work, generally unsuitable for a beginner, and IMO unlikely to work well. As I have suggested before, start by reading the literature for what others have done. Maybe your problem is solved, maybe it should not be

Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

kindly tell me sir how i can i add residue On Thu, Jun 15, 2017 at 2:04 AM, Rana Rehan Khalid wrote: > thanks justin > actually i want to know that how these values of column (atom name, type, > charge and charge group) we obtain for oxygen bonded with heme fe. is there >

Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

thanks justin actually i want to know that how these values of column (atom name, type, charge and charge group) we obtain for oxygen bonded with heme fe. is there any program through which i find the parameter file for oxygen with heme and nitric oxide with heme iron. if i just add the atom name

Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

On 6/14/17 12:25 AM, Rana Rehan Khalid wrote: Hi I have read the chapter 5 of manual but i am confuse how can i add residue into heme atom of .rtp ff this is the coordinate due to which error come HETATM 1529 O01 HEM 187 3.996 19.101 70.594 0.00 0.00 O kindly guide me

[gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

Hi I have read the chapter 5 of manual but i am confuse how can i add residue into heme atom of .rtp ff this is the coordinate due to which error come HETATM 1529 O01 HEM 187 3.996 19.101 70.594 0.00 0.00 O kindly guide me how i can make changes in the rtp file and .atp so