Re: [AMBER] .prmtop file not saved

From: Shafaq Muzammal <>
Date: Tue, 30 May 2017 08:40:28 +0000

Dear dac,

Thank you for the quick response. It worked.

Thanks again,


From: David Case <>
Sent: Wednesday, May 24, 2017 4:34:18 AM
To: AMBER Mailing List
Subject: Re: [AMBER] .prmtop file not saved

On Tue, May 23, 2017, Shafaq Muzammal wrote:
> Can anybody
> suggest how it should be dealt with as i dont want leap to read any of
> my LYS as CLYS or NLYS?

Edit (a copy of) the leaprc.ff14SB file to change the addPdbResMap array
to not convert terminal lysines to NLYS and CLYS.

(Note that this step is not needed in AmberTools16/17, since the protein
and water/ions files are no longer in the same leaprc.file.)


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Received on Tue May 30 2017 - 02:00:03 PDT
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