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

From: vedat durmaz <>
Date: Fri, 04 Jun 2010 16:14:40 +0200

case schrieb:
> On Fri, Jun 04, 2010, vedat durmaz wrote:
>> 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
>> solvent.
>> 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
> Don't worry about that is misleading.
>> +---Tried to superimpose torsions for: *-C3-C2-*
>> +--- With Sp3 - Sp0
>> +--- Sp0 probably means a new atom type is involved
> You should check the atom types for atoms C2 and C3 (use the "desc" command in
> tleap). The reference to "sp0" usually means a missing atom type.
> desc C3N
UNIT name:
Head atom: null
Tail atom: .R<C3N 1>.A<C3 3>
R<C3N 1>

the output seems to be ok. the atom types YN (N1), YC (C2), CT (C3), HC
are defined in the frcmod file and are consistent with the names in the
prep and pdb files. there's nothing unknown!

i'm confused after having saved a lib file with

saveoff C3N ch3cn.lib

its "!entry.C3N.unit.connectivity" section only shows ONE line (single
bond) for N1-C2. in contrast, having used

addAtomTypes { { "YC" "C" "sp2" } { "YN" "N" "sp2" } }

instead, results in 2 lines (=double bond) for N1-C2 in the
"!entry.C3N.unit.connectivity" section of the lib file.

and using

bond C3N.1.C2 C3N.1.N1 "T"

in order to create a triple bond leads to a software crash at

saveAmberParm C3N ch3cn.prmtop ch3cn.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
!FATAL ERROR----------------------------------------
!FATAL: In file [unitio.c], line 1778
!FATAL: Message: 1-4: cannot add bond 1 2
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.

but there are no further bond specifications in the pdb file! where else
could be further bond informations?? under these circumstances, i'm not
able to add bonds withe the "bond" command.

however, i still cannot create triple bonds. is there any way to do so?
if not: why not? does it play any role for the simulation, if the force
constants/parameters remain the same?

many questions, i know, but the whole amber mailing list archiv doesn't
seem to clear up at this point ...

> That said, none of what you posted is an error -- everything may be OK.
> ....dac
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Received on Fri Jun 04 2010 - 07:30:04 PDT
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