Re: [AMBER] how to stop making terminal residue

From: Dr. Anselm Horn <>
Date: Wed, 12 Jan 2022 10:01:00 +0100


maybe also something I have used for proteins might work here, namely
giving the explicit residue names of the structure during loading the
pdb file.

loadpdbusingseq (see. Amber21 manual p. 246, section 14.6.28.).

One had to explicitely give the names of the terminal amino acid
residues to make them ionic like in the sequence command, so the same
may apply to loading the nucleic bases, although I never tested that.

(To overcome the problem of large sequence inputs resulting from
DNA-protein-ligand systems, one could probably setup different pdb files
and load them via different commands into different units in leap,
followed by a combine-command, but I haven't tested that approach neither.)

This solution would not change the force field definition leaving leap's
conversion behaviour as it is, but was not as concise as David's
suggestion, of course.

Best regards,


Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)

Am 11.01.2022 um 17:06 schrieb David A Case:
> On Tue, Jan 11, 2022, Daniel Konstantinovsky wrote:
>> Sure! Here is the pdb (below). The first DA is the one that tleap insists
>> should be a terminal DA5, but is really a regular DA that will be
>> connected
>> to the STE residue via a tleap bond.
> At the time of loading the pdb, tleap has no way to know that the first DA
> residue is not a terminal one.
> Here's how to fix that:  after you source your leaprc files, add the
> following lines to the tleap script:
> addPdbResMap {
>   { 0 "DA" "DA"  }
> }
> This tells tleap to treat a 5' terminal ("0") DA as DA, over-riding (I
> hope)
> the instructions in leaprc.DNA.xxxx to treat it as DA5.
> Untested, but I think the idea is fine.  You could also make a copy of
> your leaprc.DNA.xxxx file and edit the addPdbResMap lines in that.
> ....dac
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Received on Wed Jan 12 2022 - 01:30:02 PST
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