[gmx-users] topology file

Hi, Myself Abhijit Kayal,student at IITD.Is it possible to create a topology file by Amber or some other molecular dynamics software for nonstandard molecules such as n-butane and can these topology files be used in gromacs?please reply. Abhijit Kayal

[gmx-users] spc model of water

Hi, Myself Abhijit Kayal.Please anyone can give me the right topology,grompp and conf file of spc model of water. Abhijit Kayal IIT Delhi

[gmx-users] water simulation

. Abhijit Kayal IIT Delhi ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] water simulation

oupl = No gen_vel = yes gen_temp = 300 gen_seed = 1993:x so what is the problem Abhijit Kayal ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-user

[gmx-users] Normal mode analysis

Hi, If I going to perform normal mode analysis of a protien molecule what are the changes have to be done in .mdp files Abhijit Kayal IIT Delhi

[gmx-users] grompp.mdp

Hi, I am going to analyse the normal mode analysis of n-butane. For this I donloaded a PDB id .Then opened in wordpad and just took the glu residue.Opend it on viewerpro and deleted the -COO, NH2,-CH2 portion to make it n-butane.Then made a pdb file and ran in GROMACS. I suceesfully created the to

[gmx-users] double precision

b4em.gro -o em.tpr -p 1OMB.top -bash: grompp_d: command not found. I am using GROMACS 4.0.4 version .So my question is why it showed like this. Thank you Abhijit Kayal IIT Delhi ___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] pdb2gmx problem

Hello everyoneI am going to analysis the PDB file 3GJN.pdb.After giving the pdb2gmx it shows the fatal error "chain identifier 'B' was used in two non-sequential blocks (residue 404, atom 3227)".So what is the solution for this. Thank you Abhijit __

[gmx-users] unit of eigenfrequency

Hi, After the g_nmeig command the mass weighted eigenfrequency is obtained.So what is the unit of this.I calculated this by GROMACS unit and it came out to be ps-1.If it is this then how to get this in general cm-i unit.Please help me.

[gmx-users] Fwd: unit of eigenfrequency

Hi, After the g_nmeig command the mass weighted eigenfrequency is obtained.So what is the unit of this.I calculated this by GROMACS unit and it came out to be ps-1.If it is this then how to get this in general cm-i unit.Please help me.

[gmx-users] normal mode analysis

Hi Gromacs User's, In the normal mode analysis if I get the first 6 eigenfrequency zero then I can think that the the protein is properly energy minimized. Thank you Abhijit ___ gmx-users mai

[gmx-users] cavity point

Hi all, I have done the normal mode analysis of pbp5 protein.Now I am looking the cavity points in this protein. There are 47 cavity points in this protein. Now is there any way to find the relationship between cavity points and the active site of the protein by analyzing the normal modes

[gmx-users] mdsimulation of drug enzyme complex

Hello everybody, I am going to simulate an enzyme complex taking a ligand at active site and another ligand at allosteric site. When I ran md simulation taking ligand at active site only then it was ok. But when I am running the simulation taking both the ligand it is showi

Re: [gmx-users] mdsimulation of drug enzyme complex

from the PRODRG server is fine. So input file may be error because GROMACS took both drug as a single one. So please help me how to take the input pdb file that it does not take a single ligand. On Fri, Apr 9, 2010 at 5:46 PM, Justin A. Lemkul wrote: > > > abhijit kayal wrote: &

Re: [gmx-users] mdsimulation of drug enzyme complex

Abhijit On Fri, Apr 9, 2010 at 6:33 PM, Justin A. Lemkul wrote: > > > abhijit kayal wrote: > >> Hi >> Thank you for your quick reply. As you mentioned I went through the >> mailing list search. And I am thinking my error occured at the system