AMBER Archive (1999)

Subject: CT atom type in leap with the weiner ff

From: Francois Dupradeau (fyd_at_u-picardie.fr)
Date: Thu Nov 18 1999 - 20:17:34 CST

Dear Amber-users,

I run leap with a Weiner_ff "leaprc" file. I just want to minimize small
organic molecules like NH3(+)CH2CH2 etc...
Then, I wrote a small leap script ; I source it :

MOL = loadpdb toto.pdb
set MOL.1.C1 type CT
etc...
saveoff MOL mol1.lib
saveamberparm MOL prmtop prmcrd

After running the script, I get this kind of "mol1.lib" file :

!!index array str
 "TAURIN"
!entry.TAURIN.unit.atoms table str name etc ...
 "C1" "" 0 1 131072 1 6 -0.518100

WITHOUT atom types for CT : I get the following error message (in the
leap.log file):

>> set TAURIN.1.C1 type CT
The value must be of the type: String

Then, (i) I write manually the right atom type in the "mol1.lib" file :

!!index array str
 "TAURIN"
!entry.TAURIN.unit.atoms table str name etc ...
 "C1" "CT" 0 1 131072 1 6 -0.518100

(ii) and run the minimization with the new mol2.lib.

Is it correct to do by this way ?
Why CT atom type is not recognized is this case (it is recognized with
the cornell ff) ?

Thanks a lot,
Regards
Francois 

-- 
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