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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Received on Tue Oct 30 2012 - 17:30:04 PDT
