Re: [AMBER] No solvent overlap

From: case <>
Date: Sat, 10 Jul 2010 10:37:51 -0400

On Fri, Jul 09, 2010, Thomas Exner wrote:
> Thank you for your help. I am using tleap from AmberTool 1.2. Perhaps I
> should switch to a newer version. Unfortunately, I do not get the script
> to run trough sleap.
> [gtkleap]$ TAQ = loadpdb 3ktq.pdb
> sleap: pertab.cpp:169: static const char*
> mort::pertab_t::get_symbol(size_t): Assertion `element != 0' failed.
> Abort

I don't see this problem with the current (version 1.4) sleap. It also has
all the ions inside the waters. [Note that in version 1.4, you need to
update residue names to the new PDB standard: for DNA, this means changing
G,C,A,T -> DG,DC,DA,DT.]

However, both tleap and sleap create some bad initial positions for the ions.
But in both cases, running 50 steps of steepest descent appeared to remove
all of these, and I think MD equilibration could continue from that point.
Since you need to do a lot of equilibration anyway, these sorts of problems
don't look fatal.

You might also want to look at the "randomizeions" command in ptraj --
probably should be used after the minimization step described above.

...good luck.....dac

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Received on Sat Jul 10 2010 - 08:00:02 PDT
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