I'm trying to set distance restraints between some protein sidechains
and a structural calcium ion. The calcium leaves its pocket and the
protein begins to unravel without any constraints. I made a upb file
and tried to use make DIST_RST and got the following error message:
makeDIST_RST -upb carestraints.upb -pdb enzph1ala_min3.pdb -rst
enzph1ala_rst_min3.rst
# makeDIST_RST
Currently configured for up to 5000 atoms
Using MAP file /usr/local/amber/dat/map.DG-AMBER
ERROR no map function for CA CA :data= 79 GLY O 171 CA CA 2.8
This is the upb file I made:
79 GLY O 171 CA CA 2.8
76 ASP OD1 171 CA CA 2.8
77 GLY O 171 CA CA 2.8
102 GLU OE2 171 CA CA 2.8
Any help would be greatly appreciated.
Kara Di Giorgio
On Apr 7, 2005, at 7:05 AM, Tim Meyer wrote:
>> In my simulational system, there are three HIS coordinated with Zn2+.
>> several MD simulation were performed with different ligands (the
>> initial conformation of Ligands is from the result of autodock).
>> I found that in one simulation three HIS residues keep a distance ~
>> 2A with Zn during 500 ps. But in some other trajectory, only two HIS
>> keep this optimal coordinated distance, ~2A.
>
> have you thought to use deprotonated HIS?
> see
>
> http://amber.scripps.edu/0Net/ions
>
> tim
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Received on Fri Apr 08 2005 - 06:53:00 PDT
