Re: AMBER: adding polar hydrogens

From: j j <fantvamp.gmail.com>
Date: Thu, 24 May 2007 13:09:04 +0200

Dear Amber User,
I'm trying to add polar Hydrogens by using protonate by doing:
protonate -d PROTON_INFO.kollua_polH < prot_in.pdb > prot_out_polH.pdb
When I check results I think HG is missing in CYS residues:
charge CYS_prot_out_polH.pdbq
ATOM 101 N CYS B 12 -13.623 -0.254 8.103 0.00 0.00 -0.520
ATOM 102 HN CYS B 12 -14.244 0.084 7.382 0.00 0.00 0.248
ATOM 103 CA CYS B 12 - 12.630 -1.259 7.786 0.00 0.00
0.146
ATOM 104 C CYS B 12 -11.306 -0.844 8.366 0.00 0.00 0.526
ATOM 105 O CYS B 12 -10.816 -1.447 9.314 0.00 0.00 -0.500
ATOM 106 CB CYS B 12 - 12.475 -1.416 6.290 0.00 0.00
0.100
ATOM 107 SG CYS B 12 -11.079 -2.451 5.880 0.00 0.00 -0.135
Total Charge -0.1350 in CYS_prot_out_polH.pdbq
I expected to have:
 charge CYS
        q[ "CYS", "N" ] = -0.5200
        q[ "CYS", "CA" ] = 0.1460
        q[ "CYS", "HN" ] = 0.2480
        q[ "CYS", "C" ] = 0.5260
        q[ "CYS", "O" ] = -0.5000
        q[ "CYS", "CB" ] = 0.1000
        q[ "CYS", "SG" ] = -0.1350
        q[ "CYS", "HG" ] = 0.1350
Total Charge 0.0000 in CYS
as especified in the q.kollua.amber
To do this I though in modifying the PROTON_INFO.kollua_polH by adding:
29,30c29,30
< CYS 6
< CA N C O CB SG

---
> CYS  7
>  CA  N   C   O   CB  SG  HG
As specified in the protonate.f:
c*****add all protons to a protein structure according to formulae
c*****specified in a PROTON_INFO file.
I'm missing again the HG so do not seem to work.
I saw this message about it in the reflector,
so I'm writting.
Thank  you,
JJ
2006/10/11, Sean Rathlef <sean.syncitium.net>:
>
>  I'm trying to add polar hydrogens to a PDB file using PROTONATE.exe(oringinally from autodock, I think).  I tried the command lines with the
> executable, but could not generate the desired output PDB file.  If anyone
> knows the proper command line calls (perhaps an example), please advise.
>
> I tried the following:
>     protonate.exe < name.pdb > out.pdb
>
> which generated:
>     PROTON_INFO, protonate.exe.stackdump, and out.pdb
>
> The only file with anything in it was the stackdump
>     Stack trace:
>     Frame     Function  Args
>     End of stack trace
>
> Do I need to use PROTON_INFO.kollua_polH, as in:
>     protonate.exe -k PROTON_INFO.kollua_polH < name.pdb > out.pdb
>
> Because I tried that, also with the "-d" flag an that didn't work either.
>
> Help greatly appreciated.
> Sean
>
>
-- 
fantvamp
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Received on Sun May 27 2007 - 06:07:21 PDT