[gmx-users] Cytochrom C

[Peter C. Lai]

Corrected bonds section (sorry been up all night)
  
 [ ACE ]
  [ atoms ]
    CH3	    CT3    -0.27    0
    HH31     HA      0.09    1
    HH32     HA      0.09    2
    HH33     HA      0.09    3
    C        C       0.51    4
    O        O      -0.51    5
  [ bonds ]
    CH3    HH31
    CH3    HH32
    CH3    HH33
    CH3    C
    C      O
 
 Surprisingly, an .hdb entry for ACE exists so you don't need to create one.
(and the .hdb entry uses HH3 as the base hydrogen name in ACE)

> 
> 
> On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote:
> > Gromos96 53A6 has it.
> > 
> > On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote:
> > > I tried charmm27 too.
> > > 
> > > Error:
> > > Residue 'ACE' not found in residue topology database
> > > 
> > > I tried all forcefield in the list provided by "pdb2gmx", but non of them
> > > works.
> > > 
> > > Dariush
> > > 
> > > 
> > > On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers <rjhamers at wisc.edu> wrote:
> > > 
> > > >    HEME is in the charmm27 force field.
> > > > bob h.
> > > >
> > > >
> > > >
> > > >
> > > > On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote:
> > > >
> > > > Yes, I have PDB file (1HRC.pdb). However, when I try to use "pdb2gmx" I
> > > > get this error:
> > > >
> > > > Residue 'HEM' not found in residue topology database
> > > >
> > > > and HEM is Iron ion inside this protein. I do not know which forcefield is
> > > > proper to use. I also tried MARTINI force field according their website; I
> > > > used martinize.py script; Again I got error.
> > > >
> > > > Regards,
> > > > Dariush
> > > >
> > > >
> > > >
> > > >
> > > > On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> > > >
> > > >>
> > > >>
> > > >> Dariush Mohammadyani wrote:
> > > >>
> > > >>>
> > > >>> Hi all,
> > > >>>
> > > >>> Has anybody made initial configuration for Cytochrom C? Can it be shared
> > > >>> with me?
> > > >>>
> > > >>>
> > > >>  There are several in the PDB.
> > > >>
> > > >> -Justin
> > > >>
> > > >> --
> > > >> ========================================
> > > >>
> > > >> Justin A. Lemkul
> > > >> Ph.D. Candidate
> > > >> ICTAS Doctoral Scholar
> > > >> MILES-IGERT Trainee
> > > >> Department of Biochemistry
> > > >> Virginia Tech
> > > >> Blacksburg, VA
> > > >> jalemkul[at]vt.edu | (540) 231-9080
> > > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >>
> > > >> ========================================
> > > >>
> > > >> --
> > > >> gmx-users mailing list    gmx-users at gromacs.org
> > > >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > >> Please search the archive at
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> > > >>
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Robert J. Hamers
> > > > Wisconsin Distinguished Professor
> > > > Univ. of Wisconsin-Madison	
> > > > 1101 University Avenue
> > > > Madison, WI 53706
> > > > Ph: 608-262-6371
> > > >  Web: http://hamers.chem.wisc.edu
> > > >
> > > >
> > > 
> > > 
> > > -- 
> > > Kind Regards,
> > > Dariush Mohammadyani
> > > Department of Structural Biology
> > > University of Pittsburgh School of Medicine
> > > Biomedical Science Tower 3
> > > 3501 Fifth Avenue
> > > Pittsburgh, PA 15261
> > > USA
> > 
> > > -- 
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> > 
> > -- 
> > ==================================================================
> > Peter C. Lai			| University of Alabama-Birmingham
> > Programmer/Analyst		| KAUL 752A
> > Genetics, Div. of Research	| 705 South 20th Street
> > pcl at uab.edu			| Birmingham AL 35294-4461
> > (205) 690-0808			|
> > ==================================================================
> > 
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> -- 
> ==================================================================
> Peter C. Lai			| University of Alabama-Birmingham
> Programmer/Analyst		| KAUL 752A
> Genetics, Div. of Research	| 705 South 20th Street
> pcl at uab.edu			| Birmingham AL 35294-4461
> (205) 690-0808			|
> ==================================================================
> 
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-- 
==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
==================================================================