Hello,
So I think I might have a solution for you. You don't want to mess
with internal residue numbering, but cpptraj also keeps track of what
I've for better or worse called "original" or "pdb" residue numbering.
You can change this at will without any effect other than changing
what gets printed to pdb/mol2 files in the residue number column. You
can use the 'change' command to change the "original" residue
numbering, then use the ':;' mask token (colon followed by semi-colon)
to select residues based on that. So for example, I tested changing
the first 3 "original" residue numbers of trpzip2 (one of my all-time
fave test systems) to 1 and it seems to work well:
Input:
parm tz2.parm7
trajin tz2.nc 1 1
change oresnums of :1 min 1 max 1
change oresnums of :2 min 1 max 1
change oresnums of :3 min 1 max 1
change oresnums of :4-13 min 2 max 11
resinfo :;1
Output (some of it anyway):
[change oresnums of :1 min 1 max 1]
Using topology: tz2.parm7
:1 selects 1 residues.
Original (output) res #s: 1 to 1 (1)
Changing original res# of residue SER:1 from 1 to 1
[change oresnums of :2 min 1 max 1]
Using topology: tz2.parm7
:2 selects 1 residues.
Original (output) res #s: 1 to 1 (1)
Changing original res# of residue TRP:2 from 2 to 1
[change oresnums of :3 min 1 max 1]
Using topology: tz2.parm7
:3 selects 1 residues.
Original (output) res #s: 1 to 1 (1)
Changing original res# of residue THR:3 from 3 to 1
[change oresnums of :4-13 min 2 max 11]
Using topology: tz2.parm7
:4-13 selects 10 residues.
Original (output) res #s: 2 to 11 (10)
Changing original res# of residue TRP:4 from 4 to 2
Changing original res# of residue GLU:5 from 5 to 3
Changing original res# of residue ASN:6 from 6 to 4
Changing original res# of residue GLY:7 from 7 to 5
Changing original res# of residue LYS:8 from 8 to 6
Changing original res# of residue TRP:9 from 9 to 7
Changing original res# of residue THR:10 from 10 to 8
Changing original res# of residue TRP:11 from 11 to 9
Changing original res# of residue LYS:12 from 12 to 10
Changing original res# of residue NME:13 from 13 to 11
[resinfo :;1]
3 residues selected.
#Res Name First Last Natom #Orig #Mol C I
1 SER 1 13 13 1 1
2 TRP 14 37 24 1 1
3 THR 38 51 14 1 1
Hope this helps,
-Dan
On Thu, Dec 17, 2020 at 5:29 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> Would there be any obvious problem with renumbering AAs in a peptide to a single residue number?
>
> LEaP output for a 4 AA peptide gives residues 1-4 as one molecule. Changing this to residue 1 for all AAs, can this cause any unintended/unexpected issues?
>
> Best regards
> // Gustaf
>
>
>
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Received on Thu Dec 17 2020 - 09:00:03 PST
