> solvatebox complex TIP3PBOX 10.0
> solvateBox: Argument #2 is type String must be of type: [unit]
Try 'list' in leap to see what the correct name of the water box might be.
Bill
On 9/20/17 11:02 AM, Rana Rehan Khalid wrote:
> I use solvatebox command for applying boundary condition these command i
> use
> source leaprc.protein.ff14SB
> source leaprc.gaff
> loadamberparam 1DX.frcmod
> loadoff idx.lib
> complex = loadpdb hbay.pdb
> now I want to add these through tleap but gives error
>
> solvatebox complex TIP3PBOX 10.0
> addions complex Na+ 0
> addions complex Cl- 0
>
> this error comes
>
> solvateBox: Argument #2 is type String must be of type: [unit]
> usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
>
> then i shall go for
> saveamberparm complex hbay.prmtop hbay.inpcrd
>
> kindly help me to correct the code for solvatebox
>
> thanks
>
>
> On Wed, Sep 20, 2017 at 9:57 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
>
>> One more thing when I load the prmtop file and then mdcrd file in the vmd
>> it showed nothing.
>>
>> Kindly guide whats the problem here thanks
>>
>> On Wed, Sep 20, 2017 at 9:46 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
>> wrote:
>>
>>> I have protein that consist of bay ligand. I follow the antechamber
>>> tutorial for protein ligand. I extract the ligand and reduced it after that
>>> I produced mol2 file of ligand then by using AM1-BCC charge model.
>>> Then i produced frcmod file my ligand frcmod file have no missing
>>> parameter for bond angle and dihedral. It have 7 missing parameters for
>>> improper. I also attached the frcmod file kindly check and guide if it is
>>> right.
>>>
>>> Then i use this script for producing prmtop and inpcrd for ligand (non
>>> standred residue)
>>>
>>> then i prepared the prmtop and inpcrd file for protein complex. BUT this
>>> file work for NBT=0, not work for periodic boundary conditions. How I can
>>> make it workable to run periodic boundary simulation because i want to
>>> compare this simulation with other simulation by employing similar flag
>>> commands.
>>>
>>> Kindly guide
>>>
>>> Thanks
>>>
>>
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Received on Wed Sep 20 2017 - 11:30:02 PDT
