[gmx-users] Cytochrom C
Krzysztof Kuczera
kkuczera at ku.edu
Fri Jan 6 19:59:56 CET 2012
Here is the blocking group from
gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp
KK
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 1
HH32 HA 0.090 2
HH33 HA 0.090 3
C C 0.510 4
O O -0.510 5
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
On 1/6/12 12:40 PM, Peter C. Lai wrote:
> 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
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
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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 |
>> ==================================================================
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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--
Krzysztof Kuczera
Professor
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
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