I got a error after running
makeDIST_RST -upb 7col.dist -pdb 2hbs.pdb -rst RST.dist
------------------------------------------------------------
ERROR no map function for CA ARG :data= 1365 ARG CA 654 GRA C 60.0
in the 7col.dist file, I have
---------------------------------------
1365 ARG CA 654 GRA C 60.0
-----------------------------
So I changed CA to CD according to map.DG-AMBER file and I have agiain,
----------------------------------------------------------------
ERROR no map function for C GRA :data= 1365 ARG CD 654 GRA C 60.0
-----------------------------------------------------------------
How do I have map function for carbon from GRA residue made by antechamber?
Bongkeun Kim
Quoting Bongkeun Kim <bkim.chem.ucsb.edu>:
> Hello Jason,
>
> I started with the simple thing first.
> I just picked up one carbon atom on surface (reg name=GRA, reg # 1153).
> And chose C aplha from the center residue(#22) of my peptide.
> And run makeDIST_RST
>
> makeDIST_RST -upb 7col.dist -pdb 2hbs.pdb -rst RST.dist
>
> in the 7col.dist file, I have
> ---------------------------------------
> 22 ARG CA 1153 GRA C 50.0
> -----------------------------
> with the max distance <50A
>
> Do you think this is a correct way to set up the distance restraint?
> Thank you.
> Bongkeun Kim
>
>
> Quoting Jason Swails <jason.swails.gmail.com>:
>
>> You can use the nmropt functionality. See the description in Chapter 6 in
>> the amber11 manual (the functionality is the same in amber10 as well).
>>
>> Good luck!
>> Jason
>>
>> On Mon, Dec 6, 2010 at 4:40 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
>>
>>> Hello,
>>>
>>> I'm going to use the implicit solvent MD study of peptide on surface.
>>> Because of absence of the periodic boundary condition, I want to give
>>> a distance restraint between flat surface molecule and the peptide
>>> whose maximum distance between the centers of mass will be less than
>>> 20Angstrom.
>>> Do you have any idea how to set this up?
>>> Thank you.
>>> Bongkeun Kim
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>
>
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Received on Mon Dec 06 2010 - 16:00:02 PST
