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
