Thanks very much for your reply, Prof. Case. I know it's been a while
since I first e-mailed the list, but I wanted to follow up.
I've attached a MOL2 file for 1-butanol, which I process with the
command:
parmchk -i orig901.mol2 -f mol2 -o orig901.frcmod
The output I get is below. The zero force parameters are problematic.
> remark goes here
> MASS
> C.3 0.000 0.000 ATTN, need revision
> H 1.008 0.161 same as hn
> O.3 0.000 0.000 ATTN, need revision
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
>
> NONBON
> C.3 0.0000 0.0000 ATTN, need revision
> H 0.6000 0.0157 same as hn
> O.3 0.0000 0.0000 ATTN, need revision
I think I know what the issues could be, but can anyone tell me:
1) Does parmchk require GAFF atomtypes? Or another atomtype format?
2) Does parmchk actually read the bond information in the mol2 file?
3) Do the atom names (field 2) need to be different for each atom,
e.g. H1, H2, ... H10?
More generally, I am able to produce MOL2 files of arbitrary molecules
with (a) SYBYL atom type information and (b) bond information that I
deem trustworthy. What is the best way to obtain an FRCMOD file, and
then a PARM7 file, for later use with NAMD?
Many thanks for any help/information that list members are able to
provide!
Best regards,
Nicholas Musolino
---------------------------------------------------------------------------
Dept. of Chemical Engineering
musolino.mit.edu | 617-253-6675 | Room E19-528
Received on Fri Apr 17 2009 - 01:10:55 PDT
