[AMBER] Solvate and manipulate order of atoms in Leap

From: He, Amy <he.1768.buckeyemail.osu.edu>
Date: Sun, 25 Jul 2021 22:26:06 +0000

Hello Amber Community,

I’m using Amber/20 and I’m doing system preparation with the leap program. I want to solvate the system, add ions, and I have to change the order of a few atoms in the structure, and generate new inputs with the re-ordered system.

Thus, I tried to do this in three steps.

  1. Solvate, add ions and save the structure of the solvated system. Here’s the tleap.in:
source leaprc.constph

complex = loadPDB cry_system.pdb
loadAmberParams frcmod.ionsjc_tip3p

solvateOct complex TIP3PBOX 12.0 0.75
addIonsRand complex Na+ 52 Cl- 45

savepdb complex solvated_system.pdb


  1. Re-order atoms in solvated_system.pdb
  2. Generate the prmtop and rstart file with the re-ordered system. Here’s the other tleap.in:
set default reorder_residues off

source leaprc.constph

complex = loadPDB reordered_system.pdb
loadAmberParams frcmod.ionsjc_tip3p

saveAmberParm complex reordered_system.parm7 reordered_system.rst7


However, I didn’t find the BOX information in my parm7 (prmtop) file. And I think it’s because I didn’t set the box in the second leap step, by either “setbox” or “solvatebox”…

My questions are:

  1. How can I retrieve the box information of the re-ordered system? Is it ok to copy the box dimensions from the parm7 file which might be generated from the solvation step?
  2. What do you usually do to obtain the proper box dimensions for an already solvated system (like a custom solvent box)?

My apologies for the multiple posts. Thank you for your time and kind advice in advance!


Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
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Received on Sun Jul 25 2021 - 15:30:02 PDT
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