Hi all,
I generated parameters for GTP with:
antechamber -i GTP_in.pdb -fi pdb -o GTP_bcc.prep -fo prepi -nc -4 \
-rn GTP -at amber -c bcc
Thanks to our sysadmin (who spend a day to compile mopac7 on a (virtual)
redhat 6.2 machine) I could now use the mopac charges - technically
everything looks fine. But unfortunately the charges don't really make sense
(not to me at least). Furthermore the charges are very different between the
mopac output and the prep / pdb.
Have a look at the phosphates (equivalent atoms get different charges, oxygen
with positive charge, P with -1.0000)
ANTECHAMBER_MUL.OUT
....
ATOM NO. TYPE CHARGE ATOM ELECTRON DENSITY
1 P -1.0000 6.0000
2 O -.3932 6.3932
3 O -.3678 6.3678
4 O .6808 5.3192
5 P 2.6773 2.3227
6 O -1.2583 7.2583
7 O -1.2465 7.2465
8 O -1.2695 7.2695
GTP_bcc.prep (last column is charge)
....
4 O1G O M 3 2 1 1.540 111.208 180.000 -0.122
5 PG P M 4 3 2 1.470 100.546 75.040 -2.143
6 O2G O E 5 4 3 1.442 110.161 41.203 -0.048
7 O3G O E 5 4 3 1.541 107.554 -67.272 1.000
8 O3B OS M 5 4 3 1.633 112.485 173.395 -0.802
9 PB P M 8 5 4 1.650 124.043 -176.128 1.620
....
Any idea anyone, what could have gone wrong here?
Thanks in advance for any comments!
Raik
BTW: Gasteiger charges look o.k. but are apparently not recommended for MD.
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Received on Thu May 13 2004 - 19:53:00 PDT
