AMBER Archive (2007)Subject: Re: AMBER: adding polar hydrogens
From: j j (fantvamp_at_gmail.com)
Date: Thu May 24 2007 - 08:00:12 CDT
With this now seems to work:
31c31,32
< 0
---
> 1
> 7 6 5 1 HG
2007/5/24, j j <fantvamp_at_gmail.com>:
>
> 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_at_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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