Re: [AMBER] error

From: Jason Swails <>
Date: Mon, 11 May 2015 15:00:11 -0400

On Mon, May 11, 2015 at 2:52 PM, George Tzotzos <> wrote:

> I’m trying to find deltaG of a homodimer.
> The dimer contains chains A (res 1-125) and B (res 127-151), two conserved
> water molecules (res 153,154) and two ligands (res 126, res 152).
> I used to generate new topologies:
> -p complex_solv.prmtop -s :126,252-254,WAT,Na+ -c
> subA-subB.prmtop -m :1-125 -r subA.prmtop -l subB.prmtop --radii=mbondi2

​I'll just point out that this gets rid of the conserved waters, in case
you didn't know that (since you stripped all WAT residues).

> I tried to run (serial) for a short 10 frame trajectory as test.
> -O -i -o FINAL_RESULTS_MMPBSA.dat -sp
> complex_solv.prmtop -cp subA-subB.prmtop -rp subA.prmtop -lp subB.prmtop -y

​What is "strip_mask" set to in your file? It *should* be the
same as what you fed to via the "-s" flag. If it's not,
then only waters and ions will get stripped, and the resulting complex
trajectory will not match the complex prmtop you generated above.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon May 11 2015 - 12:30:03 PDT
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