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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