AMBER Archive (2008)

Subject: Re: AMBER: Tough time with antechamber

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Jan 24 2008 - 09:23:08 CST

The geometry is bad. The distance between HD and CD is 1.418. Antechamber
does not assume a bond formed between the two atoms. This is why you could
not go through bond type assignment. Just convert the pdb file to a mol2
file with flag -j 5 (omit bond type assignment) and then manually add this
bond. You also need to revise the total number of bond which is the second
number in a line like "22 20 1 0 0"

Best

Junmei

On Jan 24, 2008 1:29 AM, David Cerutti <dcerutti_at_mccammon.ucsd.edu> wrote:
22 20 1 0 0

> 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
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