[AMBER] tleap: C-N triple bond and sp1 hybridization

From: vedat durmaz <durmaz.zib.de>
Date: Fri, 04 Jun 2010 14:26:46 +0200

hi there,

this is my first mail to the amber mailing list ...

i'm trying to use an acetonitrile residue (prep/frcmod/pdb, downloaded
from the manchester site, modified a little) in tleap in order to
produce .inpcrd/.prmtop files and simulate a system with acetonitrile as

when i add two new atom types as follows in tleap with sp1 hybridization
(C-N) and load my pdb file i get an error message. (in contrast, it
works well with atom types sp2-sp2).

> addAtomTypes { { "YC" "C" "sp1" } { "YN" "N" "sp1" } }
> C3N=loadpdb ch3cn.pdb
Loading PDB file: ./ch3cn.pdb
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C3-C2-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
  total atoms in file: 6

the error suggests, that sp1-sp1 bonds are not supported, but when i
have look in the the gaff atom type's list here


i can clearly find sp1 nitrogens and carbons (N1, C1). am i doing
something wrong? where should i put the information about triple bonds
in my system in order to be able to save my .inpcrd/.prmtop files? or
is there indeed no alternative to using the sp2 hybridization and a
double bond instead for my simulation?

thanks so far


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Received on Fri Jun 04 2010 - 05:30:04 PDT
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