AMBER Archive (2004)

Subject: AMBER: antechamber/Mopac: strange GTP charges

From: Raik Grünberg (graik_at_web.de)
Date: Thu May 13 2004 - 12:57:06 CDT


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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