Re: [AMBER] Partitioning issue of sander

From: 板界6柑哲彦 <>
Date: Tue, 17 Apr 2012 21:30:59 +0900

Dear Jason and David,

Thank you for your detailed explanations.

First of all, concerning your following question;

> P.S. If you are modifying topology files by hand, all bets are off, and
> your problem could be anything. I highly suggest against modifying
> topologies by hand -- try using ParmEd instead. It has many options for
> customizing and modifying topology files in a way that should continue to
> work with Amber programs.

To modifying our topology files, I used Bond LeAP to make

bonds between Fe and His/O2 (this system is hemoglobin).

In the absence of these bonds, sander ran on our 32-core parallel

computer (in the presence of the bonds, this topo file did not

work on more than 8-core computers).

According to your suggestions, I have used ParmEd and have

found the following errors;

> setBond :83.NE2 :575.FE 60 2.01

> outparm

 Outputting Amber topology file

MoleculeError: Molecule atoms are not contiguous!

These are input and output.

> This is a strange error, and one I've never seen with any of my systems.
> To me, what this implies is a strange topology. Since I don't know any
> details about how you created your topology file, I will simply provide as
> much information about what causes this error as I can.

As I showed you above, I made bonds between Fe and His/O2
in hemoglobin. If you could let me know the reasons of the results,

I would much appreciate it.

> (Did you try modifying the topology file yourself?)

As I showed you, I did not modify the files by hand.

> If you don't know which explanation is correct, try turning off constant
> pressure (if constant pressure wasn't on, then it's the first
> If the problem goes away after turning off constant pressure, I would
> venture to say it's probably the first.
> Also, try running the simulation with pmemd. If you still get problems
> with pmemd (I've gotten segfaults using topologies with a bad
> ATOMS_PER_MOLECULE section with pmemd), it's probably the second issue
> (since pmemd has a completely different parallel scheme). If pmemd works,
> it's probably the first issue.

Thank you for your detailed advises. Although I have not yet
tried these issues, I will do them, if these are needed to know

my current situations.

> If it's the second issue, there is a topology file 'doctor' of sorts
> packaged with AmberTools 12 called ParmEd. Having noticed that LEaP
> occasionally borks the ATOMS_PER_MOLECULE definition, I added a command to
> fix topology files that have this issue. Instructions for running ParmEd
> and the ParmEd GUI are in the AmberTools manual.

Can I ask weather this command means setBond
in ParmEd ?

Thank you again for your kind suggesttions.

best regards,

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Received on Tue Apr 17 2012 - 06:00:04 PDT
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