Does it mean, that the itp file, generated by the PRODRG server should only used with the gmx forcefield, or may it be combined with the other gromos frocefields, like the G43a2?On 6/13/06,
Mark Abraham <[EMAIL PROTECTED]> wrote:
Dongsheng Zhang wrote:> Sear Mark,>> Since PRODRG server only gener
What I asked is, if I have to reorganise the pdb file, or renumber the residues, etc.On 6/13/06, Mark Abraham <
[EMAIL PROTECTED]> wrote:Tamas Horvath wrote:> So if I generate an .itp with PRODRG, and link it in the .top file, then
> grompp can use the original .pdb file? Or it's not that simple?Th
Dongsheng Zhang wrote:
Sear Mark,
Since PRODRG server only generates a itp file by using gromos type force
field, do I have to use gromos force field for my whole protein-ligand
system if my ligand force field parameters are got from PRODRG? In
another word, can I mix two different force field (
Tamas Horvath wrote:
So if I generate an .itp with PRODRG, and link it in the .top file, then
grompp can use the original .pdb file? Or it's not that simple?
The order of the [ molecules ] section will have to correspond to the
order in the structure file you supply with -c to grompp, but if y
Hi,
On Monday 12 June 2006 17:25, Dongsheng Zhang wrote:
> Sear Mark,
>
> Since PRODRG server only generates a itp file by using gromos type force
> field, do I have to use gromos force field for my whole protein-ligand
> system if my ligand force field parameters are got from PRODRG? In
> another
So if I generate an .itp with PRODRG, and link it in the .top file, then grompp can use the original .pdb file? Or it's not that simple?On 6/12/06, Alan Dodd
<[EMAIL PROTECTED]> wrote:It's entirely possible to mix and match forcefield
files to create a hybrid forcefield - the lipidforcefield I use
It's entirely possible to mix and match forcefield
files to create a hybrid forcefield - the lipid
forcefield I use has OPLS parameters for the
headgroups, custom parameters for lipid tails, and GMX
parameters for everything else. As long as the hybrid
forcefield is internally consistent, it will
Sear Mark,
Since PRODRG server only generates a itp file by using gromos type force
field, do I have to use gromos force field for my whole protein-ligand
system if my ligand force field parameters are got from PRODRG? In
another word, can I mix two different force field (one for protein, one
for
I think you can use editconf to convert your original pdb to a gro file.
On Mon, 2006-06-12 at 13:48 +, Tamas Horvath wrote:
> As I understand, if there are "special" molecules in a pdb file,
> pdb2gmx cannot convert it. However, PRODRG can create an *.itp file
> for that molecule, so that I
Tamas Horvath wrote:
As I understand, if there are "special" molecules in a pdb file, pdb2gmx
cannot convert it. However, PRODRG can create an *.itp file for that
molecule, so that I can include it in the generated topology file. But
how can I place the molecule in it's original position? Or ev
As I understand, if there are "special" molecules in a pdb file, pdb2gmx cannot convert it. However, PRODRG can create an *.itp file for that molecule, so that I can include it in the generated topology file. But how can I place the molecule in it's original position? Or even better, how can I conv
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