Many thanks Jason.
Have a good weekend
George
On Apr 9, 2011, at 7:05 PM, Jason Swails wrote:
> Hi George,
>
> In this case, you just have to check that the parameters found by parmchk
> are "reasonable". $AMBERHOME/dat/leap/parm/gaff.dat has comments next to
> each atom type that describes what atom type it's supposed to be. What
> parmchk did was determine that there were atom types "similar" to the ones
> in your ligand that had parameters associated with them, so it just used
> those. If the choices were good ones, just load the frcmod and run with it.
>
> There are times when parmchk can't find what it considers reasonable
> parameters. In that case, it just gives 0.000 as every parameter and says
> ATTN next to it. That's when you *know* you need to modify it.
>
> Hope this helps,
> Jason
>
> On Sat, Apr 9, 2011 at 1:32 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>
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>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Sat Apr 09 2011 - 12:00:02 PDT
