Look into the PROTON_INFO.Brook file,
the following is the atom names of ARG residue.
I think you should mannually modify your pdb file, and make the atom
types match.
ARG 11
CA N C O CB CG CD NE CZ NH1 NH2
7
12 1 2 3 5 HA
2 5 1 6 2HB 1HB
2 6 5 7 2HG 1HG
2 7 6 8 2HD 1HD
8 8 7 9 HE
9 10 9 8 11 1HH1 2HH1
9 11 9 8 10 1HH2 2HH2
Regards,
Yang
On Tue, Oct 05, 2004 at 07:44:05PM +0200, Richard Stefl wrote:
> bugfix.39 to protonate (AMBER 7.0) causes that some atoms are assigned
> as "mystery protons" and are removed from the output. In my case:
> OH TYR 22 8.39 5.73 -5.09
> HH TYR 22 8.81 6.31 -5.75
> NH1 ARG 67 0.00 5.10 8.94
> HH11 ARG 67 0.17 5.91 9.50
> HH12 ARG 67 -0.09 4.20 9.37
> NH2 ARG 67 -0.31 4.16 6.93
> HH21 ARG 67 -0.31 4.23 5.91
> HH22 ARG 67 -0.41 3.27 7.37
>
> linux> protonate -p -k -d $AMBERHOME/dat/PROTON_INFO.Brook -i test.pdb -o
> test.prot.pdb
>
> Is there any workaround....?
>
> thank you very much in advance,
> Richard Stefl
--
I have no words to say.
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Received on Tue Oct 05 2004 - 21:53:00 PDT
