Hi Samuele,
Did you run parmchk on the resulting prep file to generate an frcmod file
and then load this into leap?
See the following tutorial for details:
http://amber.scripps.edu/tutorials/basic/tutorial4/index.htm
All the best
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Samuele Giani
> Sent: Tuesday, March 04, 2008 00:47
> To: amber.scripps.edu
> Subject: AMBER: missing gaff parameters
>
> Dear All!
>
> I'm trying to build a topology file for an organic molecule
> using gaff.
> My problem arises from the fact that some parameters are missing: what
> I've tried to do is to look into the file gaff.dat to see if I could
> generate the values with something else mimicking the types
> but I've got
> no chance. Without going for a complete reparametrization, could
> somebody be so kind to help me suggesting the parameter to use?
>
> Thank you in advance, Samuele
>
> The molecule .lib is in annexe (rm .xxx extension)...
>
> Could not find angle parameter: ca - c3 - n
> Could not find angle parameter: n3 - c3 - ca
> Could not find angle parameter: ca - ce - nh
> Could not find angle parameter: ca - ce - nh
> Could not find angle parameter: nh - ce - nh
>
> ** No torsion terms for ca-ca-ce-nh
> ** No torsion terms for ca-ca-ce-nh
> ** No torsion terms for ca-ce-nh-hn
> ** No torsion terms for ca-ce-nh-hn
> ** No torsion terms for ca-ce-nh-hn
> ** No torsion terms for ca-ce-nh-hn
> ** No torsion terms for nh-ce-ca-ca
> ** No torsion terms for nh-ce-nh-hn
> ** No torsion terms for nh-ce-nh-hn
> ** No torsion terms for hn-nh-ce-nh
> ** No torsion terms for hn-nh-ce-nh
> ** No torsion terms for nh-ce-ca-ca
>
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Mar 05 2008 - 06:07:33 PST
