[gmx-users] Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)

[fulya caglar]

Hi Mark,
  Two months ago I send a mail to Gromacs user to leran how I generate the .itp file and Tsjerk told me that I should use pdb2gmx.So I used it!Could you tell me how can I prepare 
  .itp file,please?My time is running out and my supervisor wait for some results from me!!
   
  Thanks very much!!!
  Fulya 
   
   
  >Hi Fulya,

>If your ligand is a protein, then use pdb2gmx!
>There's nothing special with 'being a ligand', and it's certainly not
required to run it through PRODRG, because someone decided that part
was to be called ligand, whereas the other part was not.

Tsjerk

On 7/3/07, fulya caglar <fulyacaglar at yahoo.com> wrote:
> Hi  all !
> We want to MD simulation of a protein-protein complex.We can't
 prepare itp.
> and gro files with PRODRG server.Because there are too many atoms in
 my
> ligand (which is a protein). How can we prepare the .itp and .gro
 files?Are
> there any tutorial for a protein protein complex?
>
>
> Best Regard
>  Fulya
>


Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
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