To generate a prmtop/prmcrd file from a PDB file for a new molecule
you need to generate a FF library. You might be interested in using
R.E.D. Server at http://q4md-forcefieldtools.org/REDS/; R.E.D. Server
provides to the user the hardware and software required to generate FF
libraries; then this FF library is loaded in the LEaP program to
generate the prmtop/prmcrd files;
See the global principle at:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
regards, Francois
> Hello, all I want to do is use this .pdb:
> http://pastebin.com/iquutx4h >
> to make a ".prmtop" and ".inpcrd" file so I can input it into OpenMM.
>
> I am an Intermediate C++ programmer but only know hwo to use windows. I am
> using
> the cygwin installation guide "http://ambermd.org/mswindows.html"
>
> Here is the error I am getting.
> http://pastebin.com/9XBk1BDD >
> Any idea what went wrong? I didn't update bc when I do I get this:
> http://pastebin.com/z75UuTKE
