Re: [AMBER] decompose MMGBSA error

From: David Case <>
Date: Mon, 18 Nov 2019 12:35:12 +0000

On Mon, Nov 18, 2019, Elvis Martis wrote:

>Try adding the following lines in mdread2.F90 file (can be found here
>AMBERHOME/Ambertools/src/sander) around line 1466 (before this line else
> ! write( 0,* ) 'bad atom type: ',atype ! call mexit( 6,1 ))
>else if (atype == 'MN') then
> x(l165-1+i) = 1.69d0 + 1.4d0
>> bad atom type: Mn

The error message indicates that the problem atom type is "Mn", not
"MN". I suspect that the original fix was not really activated.(?)

What leaprc.water files (or other leaprc files) did you load when you
created the prmtop file? Use the printDetails action in parmed to
examine you manganese ion to see what atom type it really has.

Note that the "MN" in standard PDB files is used for both the atom name
and the residue name. But PDB files don't have any information about
atom *types*.

...good luck....dac

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Received on Mon Nov 18 2019 - 05:00:01 PST
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