Hi Dan,
I did run parmchk on the ligand.
Here's the parmchk output
remark goes here
MASS
BOND
ANGLE
cy-c2-c3 62.700 116.520 same as c3-c2-c3
c2-cy-hc 47.030 110.490 same as c2-c3-hc
DIHE
cy-cy-c3-c3 1 0.156 0.000 3.000 same as X -c3-c3-X
cy-cy-c3-hc 1 0.156 0.000 3.000 same as X -c3-c3-X
cy-cy-c2-c3 1 0.000 0.000 2.000 same as X -c2-c3-X
cy-cy-c2-c2 1 0.000 0.000 2.000 same as X -c2-c3-X
c3-cy-c3-hc 1 0.160 0.000 3.000 same as hc-c3-c3-c3
c3-c3-cy-hc 1 0.160 0.000 3.000 same as hc-c3-c3-c3
c3-c2-cy-hc 1 0.000 0.000 2.000 same as X -c2-c3-X
c2-c2-cy-hc 1 0.380 180.000 -3.000 same as hc-c3-c2-c2
c2-c2-cy-hc 1 1.150 0.000 1.000 same as hc-c3-c2-c2
hc-cy-c3-hc 1 0.150 0.000 3.000 same as hc-c3-c3-hc
IMPROPER
c2-c3-c2-cy 1.1 180.0 2.0 Using default value
c2-ha-c2-ha 1.1 180.0 2.0 Using default value
The angle parameters that are declared as missing by "check ligand" are shown in the frcmod file. I'm a bit lost on how to manually edit this one.
Thanks again
George
On Apr 8, 2011, at 11:19 PM, Daniel Roe wrote:
> Hi,
>
> Try running parmchk on your ligand, e.g.
>
> parmchk -i caryo.mol2 -fi mol2 -o caryo.frcmod
>
> This will generate a frcmod file with the missing parameters. You
> should visually inspect these parameters to make sure they look
> reasonable. See sections "4.1.2 parmchk" and "4.2 A simple example for
> antechamber" in the AmberTools user manual for further examples.
>
> -Dan
>
> On Fri, Apr 8, 2011 at 5:07 PM, George Tzotzos <gtzotzos.me.com> wrote:
>> Hi everybody,
>>
>> I'm trying to generate ligand input files for an MD ligand/protein simulation.
>>
>> My ligand is caryophyllene (see snapshot)
>>
>> The ligand caryo.pdb has been generated with Chimera and the caryo.mol2 file with antechamber.
>>
>> Checking the unit ("check CARYO) gives the following output
>>
>>
>> Checking 'CARYO'....
>> Checking parameters for unit 'CARYO'.
>> Checking for bond parameters.
>> Checking for angle parameters.
>> Could not find angle parameter: cy - c2 - c3
>> Could not find angle parameter: c2 - cy - hc
>> There are missing parameters.
>> Unit is OK.
>>
>> I'm reluctant to continue given that the above parameters are missing.
>>
>> I'd appreciate any suggestion on solving this problem
>>
>> A good evening to all
>>
>> George
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 09 2011 - 02:00:02 PDT
