Out of the commands you posted, the 'solvatebox' command is creating
your box. See the manual for details on how this command functions.
-Dan
On Thu, Feb 23, 2017 at 7:58 AM, Subashini .K <subashinik.hotmail.com> wrote:
> Hi amber users,
>
>
> The following commands are given to generate amber topology files
>
>
> source leaprc.ff14SB
> loadAmberParams frcmod.tip4pew
> loadAmberParams frcmod.ionsjc_tip4pew
> source leaprc.gaff
> LIG = loadmol2 LIG.mol2
> loadamberparams LIG.frcmod
> check LIG
> receptor = loadPDB rec_final.pdb
> complex = combine {receptor LIG}
> set default PBRadii mbondi2
> saveAmberParm LIG LIG.top LIG.crd
> receptor = loadPDB rec_final.pdb
> saveAmberParm receptor rec.top rec.crd
> saveAmberParm complex com.top com.crd
> savepdb complex complex_gas.pdb
> charge complex
> addIons2 complex Na+ 0
> solvateBox complex TIP4PBOX 10.0
> saveAmberParm complex com_solvated.top com_solvated.crd
> savepdb complex com_solvated.pdb
> quit
>
>
> My question is what is command to decide the center and dimension of the box?
>
>
>
> Thanks,
> Subashini.K
>
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Feb 23 2017 - 06:00:03 PST
