Re: [AMBER] avoiding protein residue renumbering during tleap processing

From: David A Case <>
Date: Fri, 27 Sep 2019 16:15:22 -0400

On Fri, Sep 27, 2019, Seketoulie Keretsu wrote:
>I am using a protien with starting residue at 800. During tleap preparation
>of protein-ligand complex in tleap i noticed that the protein residues got
>renumbered with residues starting from 1. I used the command below to
>generate pdb files.
>ambpdb -p 1PLC.prmtop < 1PLC.inpcrd > 1PLC.inpcrd.pdb
> I there a way to prevent renumbering of residues during file processing?

No. But you can store the original residue numbers in the prmtop file
by using the "addpdb" option in ParmEd. Then, if you use the "-ext"
option to ambpdb, it will put the original residue numbers into the
1PLC.inpcrd.pdb file.

...hope this helps...dac

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Received on Fri Sep 27 2019 - 13:30:02 PDT
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