Dear Camila,
The number of added water molecules depends on both the solute and box sizes...
Anyway, that information is printed in the leap's log, for your case check at this line in your output:
" Added 18555 residues."
Best,
Matias
----- Mensaje original -----
De: "Camila Clemente" <camilamaraclemente.gmail.com>
Para: amber.ambermd.org, mmachado.pasteur.edu.uy
Enviados: Martes, 14 de Julio 2020 19:01:49
Asunto: [AMBER] SPLIT method doubt
Hello!
I would like to know how to calculate the number of water molecules to be
able to use SPLIT. In the example (
http://archive.ambermd.org/202002/0194.html) they state that: Water box 12Å
=> Nw ~ 7000 molecules
In my particular case tleap returns the following.
solvateoct solvcomplex TIP3PBOX 12.0
Scaling up box by a factor of 1.201123 to meet diagonal cut criterion
Solute vdw bounding box: 38.539 80.427 50.856
Total bounding box for atom centers: 109.253 109.253 109.253
(box expansion for 'iso' is 122.4%)
Solvent unit box: 18.774 18.774 18.774
Volume: 670111.666 A^3 (oct)
Total mass 368010.690 amu, Density 0.912 g/cc
Added 18555 residues.
Thanks
--
*Camila*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 15 2020 - 10:30:04 PDT
