I also just ran into the "could not find angle parameter" problem below.
It an be duplicated with a quick chimera-sketch of a dimer (Pro Arg) as
"loadpdb" input to tleap (with leaprc linked to
$AMBERHOME/dat/leap/cmd/leaprc.ff03
I also note that the NPRO charges are still not integral in Amber 12,
and there are several emails on the reflector about that, going back to
2009.
These recommended charges should probably be committed to the
distribution base libraries:
http://archive.ambermd.org/200906/0359.html
which reads:
"From: Jun Wang <jwang20.uci.edu>
Date: Tue, 16 Jun 2009 00:35:39 +0100
Dear Edyta,
The total charge of PRO should be an integer. The correct charges of H2 and
H3 are both 0.471856.
Best,
Jun Wang
"
On 10/30/2012 07:04 PM, Yu-Ming Huang wrote:
> Hi,
>
> I am using tleap to generate prmtop and inpcrd file by applying ff03ua.
> This is the command I am using
>
> $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03ua
>
> After I load pdb file and check it, I got the following error:
>
> Checking 'trx'....
> ERROR: The unperturbed charge of the unit: -0.106445 is not integral.
> WARNING: The unperturbed charge of the unit: -0.106445 is not zero.
> Warning: Close contact of 0.045902 angstroms between .R<NPRO 1>.A<H3 3> and
> .R<NPRO 1>.A<H2 2>
> Checking parameters for unit 'trx'.
> Checking for bond parameters.
> Checking for angle parameters.
> Could not find angle parameter: H - N - C2
> Could not find angle parameter: H - N - C2
> There are missing parameters.
> check: Errors: 1 Warnings: 2
>
>
> My structure is a 5-reside peptide. I can use tleap to successfully
> generate files by applying ff03 and ff99sb, however, only ff03ua doesn't
> work. Is anybody know what wrong with it?
>
> Thank you in advance,
> Mindy
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>
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Received on Tue Jun 18 2013 - 16:00:02 PDT
