Re: [gmx-users] Energy calculation

2011-03-17 Thread C.Y. Chang
ang 2011/3/16 Mark Abraham > > > On 16/03/11, *"C.Y. Chang" * wrote: > > Hi, > > I try to calculate the Hbond in the ligand and remove the duplicate atoms > in the .ndx file dumped from g_hbond. > This is the contents in the .ndx file. > > [ HBD ] > 1

Re: [gmx-users] Energy calculation

2011-03-16 Thread C.Y. Chang
ocess? And how could I get the angle and dihedral energy in the intramolecules? Thanks for your any comments. Best, Chia-yun 2011/3/14 Mark Abraham > > > On 14/03/11, *"C.Y. Chang" * wrote: > > Hi, >

[gmx-users] Energy calculation

2011-03-14 Thread C.Y. Chang
Hi, I try to calculate hydrogen bond (HB) energy. The g_energy does not have this term. And I find the g_hbond function in Gromacs. But the HB energy calculation is not in g_hbond. Therfore, I also try to dump the .ndx file including the HB_donor, HB_acceptor and HB_system from g_hbond, and perfro

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

2011-02-28 Thread C.Y. Chang
--- How should I solve the problem. Thanks for your suggestions. Chia-yun Chang 2011/2/28 Mark Abraham > > > On 02/28/11, *"C.Y. Chang" * wrote: > > Hi, > > I try

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

2011-02-27 Thread C.Y. Chang
, Chia-yun Chang 2011/2/19 Mark Abraham > 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

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

2011-02-20 Thread C.Y. Chang
help. Best, Chia-yun 2011/2/19 Mark Abraham > 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

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

2011-02-18 Thread C.Y. Chang
e? Thanks for your help. Best, Chia-yun 2011/2/19 Mark Abraham > On 19/02/2011 3:02 PM, C.Y. Chang wrote: > > Hi, > > I have tried to add > > [ position restraints ] > > > This is misspelled. Surely grompp

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

2011-02-18 Thread C.Y. Chang
1000 Chia-yun 2011/2/18 Mark Abraham > On 18/02/2011 1:13 PM, C.Y. Chang wrote: > >> Hi, >> >> I am dealing with the lipid bilayer permeation simulation. >> Most compounds can be finished, but the compounds with CN can'

[gmx-users] about -CN triple bond

2011-02-17 Thread C.Y. Chang
Hi, I am dealing with the lipid bilayer permeation simulation. Most compounds can be finished, but the compounds with CN can't be performed simulation. I have searched the discussion in the gmx-users discussion. The "vsite" has been mentioned, and I have refered to the gromacs manual. But I don't

Re: [gmx-users] GROMOS96 topology for small molecule

2011-01-19 Thread C.Y. Chang
thanks :) 2011/1/19 mohsen ramezanpour > It is on now,you can use it. > as Justin said you should validate it. > best > > > On Tue, Jan 18, 2011 at 9:37 PM, Justin A. Lemkul wrote: > >> >> >> C.Y. Chang wrote: >> >>> Hi, >>> >

[gmx-users] GROMOS96 topology for small molecule

2011-01-18 Thread C.Y. Chang
Hi, I need to obtain the GROMOS96 topology files (and including the corresponding PDB files) for some small molecules. I could obtain them from PRODRG beta server before, but the server seems to shut down now. How could I get them? or from other server or program?