Re: [AMBER] MMGBSA calculations with explicit water molecules

From: Jason Swails <jason.swails.gmail.com> Date: Sat, 20 Jan 2018 21:06:23 -0500

--
Jason M. Swails 
> On Jan 18, 2018, at 3:14 PM, Marawan Hussien <marawanhussain.yahoo.com> wrote:
> 
> Hello,I am trying to perform MMGBSA calculations for a protein ligand complex keeping few explicit water molecules as part of the receptor.I have processed the generated trajectory with cpptraj using the closest command to keep the number of waters i need. As I can understand from the manual, I need to use the "strip_mdcrd=0" command in the following way:
> ######Input file for running GB&general   startframe=50,endframe=20000,strip_mdcrd=0,interval=1,receptor_mask=:1-118:120-169,ligand_mask=:119,/&gb  igb=8, saltcon=0.150,/######
> But I keep getting this error:
> InputError: Unknown variable strip_mdcrd in &general  Enter `MMPBSA.py --help` for help
> 
> Do I miss something ? I tried different versions of AMBER (12,14,16) but none worked.
> Regards,Marawan
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