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

[Mark Abraham]

fulya caglar wrote:
> Hi Mark,
> I'm so sorry for taking so much of your time.I tried to explain how I 
> generated the sections:
>  
> Firstly I  named my ligand (protein) files as  *drg*  and my protein  
> files as *trp.*
>  
> Next I generated the drg.itp and trp.top  files with pdb2gmx
>  
> pdb2gmx  -ff gmx -f drg.pdb -o drg2 -p drg.top
> pdb2gmx  -ff gmx -f trp.pdb -o trp2.pdb  -p trp.top  -merge -ignh –ss
>  
> Then I pasted the coordinates from drg.pdb onto the end of the trp2.file 
> and I edited trp.top file; I added  #include “ drg.itp” and under the 
> [molecules] section my ligand.

pdb2gmx doesn't make .itp files, like I said two emails ago.

Mark