Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution

From: David A Case <>
Date: Thu, 2 Nov 2017 07:51:15 -0400

On Thu, Nov 02, 2017, 杨满意 wrote:

> Now I wanted to do MD simulation for A and B mixed solution.

The recommended workflow is this: use packmol or some other program to make
a single PDB file that has all the molecules you wish to have in the system.
Just use one "loadPdb" command to get this into tleap; use the "set <unit>
box..." command to tell tleap that this is a periodic simulation.

> (a) When I act the A and B as a unit, the files is like this:
> source oldff/leaprc.ff99SB
> source leaprc.gaff2
> mol= loadmol2 avmocntf2_monomer-a1.mol2
> check mol
> loadamberparams avmocntf2_monomer-a1.frcmod
> solvent = copy mol1
                      ^^^^^^ ?? what is "mol1"? is this a typo?


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Received on Thu Nov 02 2017 - 05:00:04 PDT
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