AMBER Archive (2008)

Subject: AMBER: Tough time with antechamber

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Thu Jan 24 2008 - 01:29:38 CST

Hello,

    I'm trying to run antechamber but I'm having a real tough time getting
it to work. I can run it with this file (Glycerol.pdb):

ATOM 1 CA GLL A 1 0.000 0.000 0.000
ATOM 2 HA GLL A 1 0.000 -0.629 -0.890
ATOM 3 OB GLL A 1 0.000 -0.814 1.151
ATOM 4 HB GLL A 1 0.000 -0.253 1.930
ATOM 5 CB1 GLL A 1 1.246 0.881 0.000
ATOM 6 1HB2 GLL A 1 1.286 1.509 0.890
ATOM 7 1HG3 GLL A 1 1.286 1.509 -0.890
ATOM 8 OG1 GLL A 1 2.397 0.067 0.000
ATOM 9 HG1 GLL A 1 3.181 0.622 0.000
ATOM 10 CB2 GLL A 1 -1.246 0.881 0.000
ATOM 11 2HB2 GLL A 1 -1.286 1.509 0.890
ATOM 12 2HG3 GLL A 1 -1.286 1.509 -0.890
ATOM 13 OG2 GLL A 1 -2.397 0.067 0.000
ATOM 14 HG2 GLL A 1 -3.181 0.622 0.000
END

using the command:

antechamber -i Glycerol.pdb -fi pdb -o Glycerol.prep -fo prepi -c rc -cf
charges

and things work fine (here, "charges" is just a file with a bunch of
0.000's written one per line--I'm going to fill in the charges later).

    But, if I try to run with this file (MPD.pdb):

ATOM 1 CD MPD 1 -0.147 0.417 0.005
ATOM 2 CC MPD 1 0.356 -1.005 0.005
ATOM 3 1HC MPD 1 0.963 -1.177 -0.888
ATOM 4 2HC MPD 1 0.963 -1.177 0.897
ATOM 5 CB MPD 1 -0.817 -1.953 0.005
ATOM 6 OB MPD 1 -1.605 -1.730 -1.153
ATOM 7 1HB MPD 1 -1.064 -1.883 -1.947
ATOM 8 CF MPD 1 -1.655 -1.716 1.236
ATOM 9 1HF MPD 1 -1.047 -1.888 2.128
ATOM 10 2HF MPD 1 -2.505 -2.403 1.236
ATOM 11 3HF MPD 1 -2.019 -0.686 1.236
ATOM 12 CA MPD 1 -0.314 -3.375 0.005
ATOM 13 1HA MPD 1 0.293 -3.547 0.897
ATOM 14 2HA MPD 1 0.293 -3.547 -0.888
ATOM 15 3HA MPD 1 -1.164 -4.062 0.005
ATOM 16 CE MPD 1 0.356 1.127 -1.227
ATOM 17 1HE MPD 1 1.449 1.127 -1.227
ATOM 18 2HE MPD 1 -0.008 0.612 -2.119
ATOM 19 3HE MPD 1 -0.008 2.158 -1.227
ATOM 20 OD MPD 1 0.326 1.085 1.162
ATOM 21 1HD MPD 1 0.002 0.627 1.956
ATOM 22 HD MPD 1 -1.565 0.417 0.005
END

Then, I get a mess. The command is the same, just substitute "MPD" for
"Glycerol." Can anyone offer a solution?

    Also, does anyone have some parameters for MPD? I'll go looking, but
it probably won't be too hard to obtain the charges and the rest of the
molecule looks very familiar to existing things in AMBER.

Thanks!

Dave
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu