Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

2011-03-03 Thread Mark Abraham
On 3/03/2011 11:42 PM, Justin A. Lemkul wrote: bharat gupta wrote: The residue is a chromophore of Green Fluorescent Protein. The parameter file that I have got has the connection for serine and glycine :- For those of us who aren't fluent in CHARMM (or whatever this is), it would be mor

Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

2011-03-03 Thread Pär Bjelkmar
Hi, 3 mar 2011 kl. 10.17 skrev gmx-users-requ...@gromacs.org: > but I have the torsion angles , bond angles for my residue .. The problem > is I don't know which one to put where as the charmm FF parameter that I > have got doesnot match with the charmm ff parameter in gromacs.. that's y I > am

Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

2011-03-03 Thread Justin A. Lemkul
bharat gupta wrote: The residue is a chromophore of Green Fluorescent Protein. The parameter file that I have got has the connection for serine and glycine :- For those of us who aren't fluent in CHARMM (or whatever this is), it would be more useful if you describe plainly the nature of th

Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

2011-03-03 Thread bharat gupta
The residue is a chromophore of Green Fluorescent Protein. The parameter file that I have got has the connection for serine and glycine :- !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000

Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

2011-03-03 Thread Mark Abraham
On 03/03/11, bharat gupta wrote: > Hi, > > I followed the tutorial > - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for > updating the Charmm FF for my modified residue .. > > > > I added the residues to the .rtp file , then I added the new atom types in

Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

2011-03-03 Thread bharat gupta
ROMACS users > *Sent:* Thursday, 3 March 2011 11:31:38 > *Subject:* [gmx-users] Re: adding ff parameter of modified residue to > charmm ff > > Hi, > > I followed the tutorial - > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > for > updati

Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

2011-03-03 Thread Jianguo Li
: adding ff parameter of modified residue to charmm ff Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in

[gmx-users] Re: adding ff parameter of modified residue to charmm ff

2011-03-02 Thread bharat gupta
Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and