Re: [gmx-users] How to set the inter-chain disulfind bond in martini?
Dear Peter,
Thank you, I find the answer now. Sorry I was using a pdb that the SS length is
too long to form the SS bond. After changing to a correct one, I got the
solution.
I think, if we have more than one chain, we MUST use "-merge" option, so that
the interchain SS bond can shown in the generated itp file.
If "-merge" is missing, only the intra-chain SS bonds are shown in the
individual itp files.
So happy to see the martini forum come back!
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Tue, Jan 29, 2019 11:03 PM
To: "gromacs.org_gmx-users";
Subject: How to set the inter-chain disulfind bond in martini?
Dear Martini friends,
My protein has 10 Cys with 5 disulfind bonds in light chain (LC) and heavy
chain (HC):
) Interchain disulfide bond: LC214 ?C HC220
) Intrachain disulfide of LC: LC23 ?C LC88, LC134 ?C LC194
) Intrachain disulfide of HC: HC144 ?C HC200, HC96 ?C HC22
Using this command will only generate four intrachain disulfide bonds, without
the interchain one:
$ python martinize.py -f protein.pdb -o system.top -x protein-CG.pdb -dssp
./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 -cys auto -merge L,H
prompt:
$ INFO Checking for cystine bridges, based on sulphur (SG) atoms lying
closer than 0.2200 nm
$ INFO Detected SS bridge between ('SG', 'CYS', 23, 'L') and ('SG',
'CYS', 88, 'L') (0.204094 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 134, 'L') and ('SG',
'CYS', 194, 'L') (0.204489 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 214, 'L') and ('SG',
'CYS', 434, 'H') (0.203603 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 358, 'H') and ('SG',
'CYS', 414, 'H') (0.204830 nm)
I can see the four disulfide bonds information is reflected in the [
constraints ] section of "Protein_L+Protein_H.itp" file:
$ 45 191 1 0.24000 ; Cys-bonds/special link
$ 294 431 1 0.24000 ; Cys-bonds/special link
$ 475 947 1 0.24000 ; Cys-bonds/special link
$ 778 900 1 0.24000 ; Cys-bonds/special link
So how to also ensure the intactness of the interchain disulfide bond?
You can find my files at
https://github.com/lanselibai/martini/tree/master/20190129_disulfide
Thank you!
Yours sincerely
Cheng
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Re: [gmx-users] How to set the inter-chain disulfind bond in martini?
Hi Cheng,
What’s the distance between the two interchain SG atoms? You can either tune
the distance used for autodetecting cys bonds, or just specify all of them
using the command line. Try `python martinize.py -h`
Peter
PS. The cgmartini.nl forum is also back online, which might be a better medium
for these martini specific questions.
From: ZHANG Cheng
Sent: 29 January 2019 16:08
To: gromacs.org_gmx-users
Subject: [gmx-users] How to set the inter-chain disulfind bond in martini?
Dear Martini friends,
My protein has 10 Cys with 5 disulfind bonds in light chain (LC) and heavy
chain (HC):
) Interchain disulfide bond: LC214 – HC220
) Intrachain disulfide of LC: LC23 – LC88, LC134 – LC194
) Intrachain disulfide of HC: HC144 – HC200, HC96 – HC22
Using this command will only generate four intrachain disulfide bonds, without
the interchain one:
$ python martinize.py -f protein.pdb -o system.top -x protein-CG.pdb -dssp
./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 -cys auto -merge L,H
prompt:
$ INFO Checking for cystine bridges, based on sulphur (SG) atoms lying
closer than 0.2200 nm
$ INFO Detected SS bridge between ('SG', 'CYS', 23, 'L') and ('SG',
'CYS', 88, 'L') (0.204094 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 134, 'L') and ('SG',
'CYS', 194, 'L') (0.204489 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 214, 'L') and ('SG',
'CYS', 434, 'H') (0.203603 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 358, 'H') and ('SG',
'CYS', 414, 'H') (0.204830 nm)
I can see the four disulfide bonds information is reflected in the [
constraints ] section of "Protein_L+Protein_H.itp" file:
$ 45 191 1 0.24000 ; Cys-bonds/special link
$ 294 431 1 0.24000 ; Cys-bonds/special link
$ 475 947 1 0.24000 ; Cys-bonds/special link
$ 778 900 1 0.24000 ; Cys-bonds/special link
So how to also ensure the intactness of the interchain disulfide bond?
You can find my files at
https://github.com/lanselibai/martini/tree/master/20190129_disulfide
Thank you!
Yours sincerely
Cheng
--
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[gmx-users] How to set the inter-chain disulfind bond in martini?
Dear Martini friends,
My protein has 10 Cys with 5 disulfind bonds in light chain (LC) and heavy
chain (HC):
) Interchain disulfide bond: LC214 ?C HC220
) Intrachain disulfide of LC: LC23 ?C LC88, LC134 ?C LC194
) Intrachain disulfide of HC: HC144 ?C HC200, HC96 ?C HC22
Using this command will only generate four intrachain disulfide bonds, without
the interchain one:
$ python martinize.py -f protein.pdb -o system.top -x protein-CG.pdb -dssp
./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 -cys auto -merge L,H
prompt:
$ INFO Checking for cystine bridges, based on sulphur (SG) atoms lying
closer than 0.2200 nm
$ INFO Detected SS bridge between ('SG', 'CYS', 23, 'L') and ('SG',
'CYS', 88, 'L') (0.204094 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 134, 'L') and ('SG',
'CYS', 194, 'L') (0.204489 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 214, 'L') and ('SG',
'CYS', 434, 'H') (0.203603 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 358, 'H') and ('SG',
'CYS', 414, 'H') (0.204830 nm)
I can see the four disulfide bonds information is reflected in the [
constraints ] section of "Protein_L+Protein_H.itp" file:
$ 45 191 1 0.24000 ; Cys-bonds/special link
$ 294 431 1 0.24000 ; Cys-bonds/special link
$ 475 947 1 0.24000 ; Cys-bonds/special link
$ 778 900 1 0.24000 ; Cys-bonds/special link
So how to also ensure the intactness of the interchain disulfide bond?
You can find my files at
https://github.com/lanselibai/martini/tree/master/20190129_disulfide
Thank you!
Yours sincerely
Cheng
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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