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
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Edyta Malolepsza
Sent: Monday, June 15, 2009 3:10 AM
To: AMBER Mailing List
Subject: [AMBER] total charge for NPRO in ff03ua
Dear Amber users,
I am using the united atom force field ff03ua and have come across a
problem with N-terminal proline, where total charge for the whole
residue is not integer. Here is an entry from uni_aminont03.lib. This
entry is the same both for amber9 and amber10 taken from latest
version of AMBERTools1.2 from AMBER10.
!entry.NPRO.unit.atoms table str name str type int typex int resx
int flags int seq int elmnt dbl chg
"N" "N" 0 1 131072 1 7 -0.415266
"H2" "H" 0 1 131072 2 1 0.418633
"H3" "H" 0 1 131072 3 1 0.418633
"CD" "C2" 0 1 131072 4 6 0.179220
"CG" "C2" 0 1 131072 5 6 0.048036
"CB" "C2" 0 1 131072 6 6 0.002419
"CA" "CT" 0 1 131072 7 6 0.157515
"HA" "H1" 0 1 131072 8 1 0.003120
"C" "C" 0 1 131072 9 6 0.680470
"O" "O" 0 1 131072 10 8 -0.599226
The total charge is 0.893554.
Can anybody help to explain this? All other residues have integer total
charges.
Best regards,
Edyta Malolepsza
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Received on Mon Jul 06 2009 - 09:43:20 PDT
