Thanks a lot for your ultrafast response and above all your help.
Arik
On 7/19/2010 11:20 AM, Jason Swails wrote:
> Hello,
>
> I've put my comments below.
>
> On Mon, Jul 19, 2010 at 2:04 PM, arikcohen<arikcohen.ucla.edu> wrote:
>
>> Dear Members,
>>
>> I would be most thankful for any help in the following: I'm trying to
>> set up a covalent bond between my substrate and a catalytic lysine.
>>
>> The tleap script is the following: (the substrate was named as HPD)
>>
>> source /u/local/apps.old/amber8/serial/dat/leap/cmd/leaprc.gaff
>
>> source /u/local/apps/amber/10/dat/leap/cmd/leaprc.ff99SB
>>
> The paths are not needed. Also, why are you using leaprc.gaff from amber8
> and leaprc.ff99SB from amber10? Just change these two lines to:
>
> source leaprc.ff99SB
> source leaprc.gaff
>
> That should do it.
>
>
>> loadamberprep DERACognateSub.prepin
>>
>> loadamberparams DERACognateSub.frcmod
>>
>> enzyme_design = loadpdb DERA_MonCogSub_NoH.1.pdb
>>
> Your unit name is now enzyme_design
>
>
>> set enzyme_design head LYN.167.NZ
>>
>> set HPD tail HPD.252.C6
>>
> You do not need these. Furthermore, the the atom specification should be
> "unit.residue#.atom". Your unit is enzyme_design, not the name of the
> residue. In order to create a bond, just see the "bond" command in leap.
> It seems that what you want is:
>
> bond enzyme_design.167.NZ enzyme_design.252.C6
>
>
>> check enzyme_design
>>
>> charge enzyme_design
>> .
>> .
>> .
>>
>> The output which I'm getting is the following:
>>
>> >
>> > set enzyme_design head LYN.167.NZ
>> The value must be of the type: Atom
>>
> I explained this error above, but again, this command is not needed
>
>
>> >
>> > set HPD tail HPD.252.C6
>> The value must be of the type: Atom
>> >
>> > check enzyme_design
>> Checking 'enzyme_design'....
>> ERROR: The unperturbed charge of the unit: -4.805188 is not integral.
>> WARNING: The unperturbed charge of the unit: -4.805188 is not zero.
>>
> This is pretty self-explanatory. This is almost certainly due to your
> ligand having a non-integer charge. This is not close enough to an integer
> to be round-off error (or something similar), so I would double-check your
> charge derivation method for your ligand. If you need to redo it, consider
> R.E.D. tools. There is a link to it on the amber website.
>
>
> Hope this helps,
> Jason
>
>
>> I thank you in advance for your help
>>
>>
>> Arik
>>
>>
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Jul 19 2010 - 12:00:05 PDT
