Dear amber-users,
Why there is mismatch in the number of atoms when created using "ambpdb"
and "savepdb" as follow? ambpdb gives more number of water molecules.
The pdb file created using "savepdb" gives correct number of atoms in the
system.
=====================
source leaprc.ff99SB
m = loadpdb minimized_structure.pdb
addions m Cl- 0
solvatebox m TIP3PBOX 14
saveamberparm m UVI_control_solion.prmtop UVI_control_solion.inpcrd
savepdb m UVI_solion.pdb
quit
======================
ambpdb -p UVI_control_solion.prmtop < UVI_control_solion.inpcrd > test.pdb
======================
With regards,
Sunita
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Received on Mon Sep 08 2014 - 06:30:03 PDT
