Hi
and thanks for the response so I am adding a copper ion to a histidine
and as it might have other interactions with nearby residues I have
changed the type of NE2 to UA - yhe problem is that when I have
generate the inpcrd and prmtop and look at the pdb file(ambpdb from
ambertools) the imidazole ring has lost its planarity - having a boat
shape.
I think it somehow does not read the parameters correctly I have
include the parm below - is there any syntax like new line after each
section and not tabs or something like that?
# Parameters
MASS
UA 14.01
CU 65.36
BOND
UA-CU 47.37 2.02
CC-UA 410.0 1.394
CR-UA 488.0 1.335
CV-UA 410.0 1.394
ANGLE
CU-UA-CV 14.44 126.57
CU-UA-CR 16.22 127.30
UA-CU-UB 5.98 119.89
UA-CU-UC 4.04 120.61
UA-CU-KW 6.67 105.04
CT-CC-UA 70.0 120.00
CW-CC-UA 70.0 120.00
H5-CR-UA 50.0 120.00
NA-CR-UA 70.0 120.00
CC-CV-UA 70.0 120.00
H4-CV-UA 50.0 120.00
CC-UA-CR 70.0 117.00
CR-UA-CV 70.0 117.00
CB-UA-LP 150.0 126.0
CC-UA-LP 150.0 126.0
CK-UA-LP 150.0 126.0
CR-UA-LP 150.0 126.0
CV-UA-LP 150.0 126.0
DIHEDRAL
X -CB-UA-X 2 5.10 180.0 2.
X -CC-UA-X 2 4.80 180.0 2.
X -CK-UA-X 2 20.00 180.0 2.
X -CR-UA-X 2 10.00 180.0 2.
X -CV-UA-X 2 4.80 180.0 2.
X -CR-UA-X 2 10.00 180.0 2.
X -CV-UA-X 2 4.80 180.0 2.
H4 -CB-UA-CU 2 0.0 180.0 2.
NONBON
UA 1.824 0.17
CU 1.740 1.14
On Thu, Feb 24, 2011 at 11:43 PM, David Case <dacase.rci.rutgers.edu> wrote:
> On Feb 24, 2011, at 4:00 PM, Jorgen Simonsen <jorgen589.gmail.com> wrote:
>>
>> I am trying to parametrize a novel residue with copper and is bound to
>> a nitrogen atom - I try to minimize my model but it is that through
>> xleap it does not recognize the atom types as I get the following
>> error
>>
>>
>>> loadamberparams His100/hr1.frcmod
>> Loading parameters: ./His100/hr1.frcmod
>> Reading force field modification type file (frcmod)
>> Reading title:
>> ## Parameters
>> (UNKNOWN ATOM TYPE: UA)
>> (UNKNOWN ATOM TYPE: CU)
>
> I don't these are errors, just warnings about a missing addAtom command.
>>
>> when I try to look at the structure it does not recognize the atoms -
>> they look really strange
>
> Are you sure this is more than just a visual problem? You don't say how you did the visualization, or what "really strange" means.
>
> ....dac
>>
>
>
>
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Received on Thu Feb 24 2011 - 15:30:06 PST
