Re: [AMBER] Error in saving prmtop and inpcrd

From: David Case <>
Date: Fri, 12 Jul 2019 13:40:33 +0000

On Fri, Jul 12, 2019, shivangi agarwal wrote:

>This is the leap.log file. I have also tried the above two suggestions, but
>still not working.

Your leap.log file shows a mixture of runs that worked, and some that
didn't, and it is quite hard to follow. I *think* the key problem is
that you are loading some very old files that treated Na+ as atom type
IP, and that is not compatible with present standards.

The key information we need is the exact set of commands you gave to
tleap, plus the part of the input PDB file that has Na+ ions.

(Aside to others: "Na+" itself is a non-standard identifier as an atom
or residue name, and should be changed to "NA". The only reason that
"Na+" works is that we have some special instructions in some files to try
to be backwards compatible. But other programs may not recognize such
non-standard ion names.)


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Received on Fri Jul 12 2019 - 07:00:02 PDT
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