Re: [AMBER] how to obtain index of atoms based on residue and atom masks

From: Dr. Anselm Horn <anselm.horn.fau.de>
Date: Wed, 19 Jan 2022 11:23:28 +0100

Tammy,

adding to Matthew's idea:

If you have the pdb-tools for the command line installed on your system
(pip install pdb-tools ; cf http://www.bonvinlab.org/pdb-tools/), a pdb
file of your system at hand, and a simple residue mask, then a single
command line may also yield almost all you want, provided that you just
select standard residues:

pdb_selres -<res_first:res_last> <your.pdb> | grep "^ATOM" | awk
'{printf "%1d,", $2} '; echo

Note that the last index is followed by a comma, too.
(The selection mask for pdb_selres also allows for more than just one
residue range.)

For advanced masks, however, it is certainly better to use cpptraj for
preprocessing, as Matthew suggested.

Best regards,

Anselm

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


Am 19.01.2022 um 04:12 schrieb Matthew Guberman-Pfeffer:
> Hello Tammy,
>
> One thought is that you can use the mask keyword in cpptraj to generate a file. This file, call it mask.txt, will list the atom numbers in the second column. You then can process this file with a bash script to get a comma separated list, something like the following:
>
> idx=0
> while IFS= read -r F1 <&2;do
>
> if [ $idx != 0 ];then
> atnum=$(echo $F1 | awk '{print $2}')
> echo -n “${atnum},";
> fi
>
> idx=$((idx+1))
> done 2< mask.txt
>
> Note that the line indexing (idx) is to skip the “AtomNum” header in mask.txt.
>
> Hope this work-around helps.
>
> Best,
> Matthew
>
>
>
>> On Jan 18, 2022, at 8:01 PM, Ming Tang <m21.tang.qut.edu.au> wrote:
>>
>> *Message sent from a system outside of UConn.*
>>
>>
>> Dear list,
>>
>> Is there a command to print out atom indexes (separated by comma) for a large number of residues? I want to use them as cv_i in ABMD.
>>
>> Thanks,
>> Tammy
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Received on Wed Jan 19 2022 - 02:30:02 PST