Second script is true ,"set default PBRadii mbondi3" you set after loading
the pdbfile.
On Tue, Aug 14, 2018 at 1:31 PM, 龚乾坤 <m201770109.hust.edu.cn> wrote:
> Dear amber users or developers,
>
> In GB simulations,we should add "set default PBRadii mbondi3" in tleap
> script.Following is my tleap script:
>
> script1
>
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
>
> set default PBRadii mbondi3
> CYS=CYX
> com=loadpdb 4ins.pdb
>
> solvatebox com TIP3PBOX 10
> addions com Na+ 0
>
> check com
> saveamberparm com prmtop inpcrd
>
> quit
>
> script2
>
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
>
> CYS=CYX
> com=loadpdb 4ins.pdb
> set default PBRadii mbondi3
>
> solvatebox com TIP3PBOX 10
> addions com Na+ 0
>
> check com
> saveamberparm com prmtop inpcrd
>
> quit
>
>
>
>
> So I want to know the scripts which is ture,and where should I put "set
> default PBRadii mbondi3" in tleap?
>
>
>
>
> Thank you in advance.
>
> Qiankun Gong
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Nisha Amarnath Jonniya
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Tue Aug 14 2018 - 02:00:02 PDT
