Hi,
I have a similar problem with the cz atom type in tleap of the AmberTools
1.4.
tleap doesn't save the topology files because of the error:
tleap -f leaprc.gaff -f leaprc.ff99SB
No mass defined for non-bond atom type: cz - skipping
Building topology.
Building atom parameters.
For atom: .R<LIG 298>.A<C17 19> Could not find type: cz
Parameter file was not saved.
while the frcmod file contains this atom type:
================================================
remark goes here
MASS
BOND
na-cz 411.10 1.391 same as c2-na
ANGLE
c -cc-na 69.987 114.105 Calculated with empirical approach
cc-na-cz 63.980 125.750 same as c2-na-cc
cd-na-cz 63.980 125.750 same as c2-na-cd
na-cz-na 73.650 109.330 same as na-c2-na
na-cz-nh 73.205 114.750 Calculated with empirical approach
hn-na-cz 47.620 119.280 same as c2-na-hn
cz-na-c3 64.230 117.200 same as c2-na-c3
DIHE
cc-na-cz-na 1 0.625 180.000 2.000 same as X
-c2-na-X
cc-na-cz-nh 1 0.625 180.000 2.000 same as X
-c2-na-X
cd-na-cz-na 1 0.625 180.000 2.000 same as X
-c2-na-X
cd-na-cz-nh 1 0.625 180.000 2.000 same as X
-c2-na-X
na-cz-na-c3 1 0.625 180.000 2.000 same as X
-c2-na-X
na-cz-nh-c3 1 0.675 180.000 2.000 same as X
-c2-nh-X
hn-na-cz-na 1 0.625 180.000 2.000 same as X
-c2-na-X
hn-na-cz-nh 1 0.625 180.000 2.000 same as X
-c2-na-X
c3-na-cz-nh 1 0.625 180.000 2.000 same as X
-c2-na-X
IMPROPER
c -c3-n -cd 1.1 180.0 2.0 Using default
value
n -n -c -o 10.5 180.0 2.0 General improper
torsional angle (2 general atom types)
c -c -n -c3 1.1 180.0 2.0 Using default
value
cc-n -c -o 10.5 180.0 2.0 General improper
torsional angle (2 general atom types)
c -cd-cc-na 1.1 180.0 2.0 Using default
value
cc-n -cd-na 1.1 180.0 2.0 Using default
value
cd-cz-na-hn 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
na-na-cz-nh 1.1 180.0 2.0 Using default
value
c3-cc-na-cz 1.1 180.0 2.0 Using default
value
c3-c3-nh-cz 1.1 180.0 2.0 Using default
value
ca-ca-ca-ha 1.1 180.0 2.0 General improper
torsional angle (2 general atom types)
ca-ca-ca-os 1.1 180.0 2.0 Using default
value
NONBON
cz 1.9080 0.0860 same as c2
=================================================
is there a way to resolve this error?
Best regards,
--
Shahid.
On Thu, Mar 4, 2010 at 4:56 AM, case <case.biomaps.rutgers.edu> wrote:
> On Wed, Mar 03, 2010, Barbault Florent wrote:
> >
> > Enclosed is the pdb input file and the prep output file. I use the
> following
> > command:
> >
> > antechamber -i pdb_input.pdb -fi pdb -o prep.prep -fo prepi -c bcc -rn
> LIG -nc
>
> I see the "cz" atom type, but I'm not sure this is really a problem. If
> you
> run parmchk, it will create a frcmod file with all of the needed
> parameters,
> noting that "cz" is the same as "c2".
>
> I certainly agree that it is confusing to have an atom type not in
> gaff.dat,
> but you should be able to proceed anyway, I think.
>
> ...good luck...dac
>
>
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>
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Received on Thu Jul 08 2010 - 07:00:03 PDT
