[gmx-users] Re: prodrg on small molecule

[jztan at mail.shcnc.ac.cn]

Dear gmx-users,

Maybe this is a really useless quesiontion, but I really need your help.
Thank you in advance!

I use PRODRG Beta2 to generate GORMOS96 force field on my small molecule,
but finally I found the format is still like Gromacs force field.

PRODRG Beta2 generated the results as following:
 [ bonds ]
 ;ai  aj  fu    c0          c1
   1   2   1 0.153    334720.0 0.153    334720.0 ;   C18  C13
   2   3   1 0.153    334720.0 0.153    334720.0 ;   C13  C12
.............


But in GROMOS96(43a1), should be like this:
[ bonds ]
 ;ai  aj  fu    c0          c1
     1     2     2 gb_26
     2     3     2 gb_26
............

So my question is should I change all the format as those in
GROMOS96(43a1) style? If so, some of the bonds are not defined in
GROMOS96(43a1), so I should add these missing bonds into it manually,
right?

Thank you for any reply.

Jinzhi
2005-10-17