Topic Options
#37512 - 05/30/19 02:53 PM delete disulfide bond without alterng membrane protein sysm
Binod Offline
Forum Member

Registered: 09/27/16
Posts: 8
Loc: New York, New York
Hello Charmm Users,
I have one equilibrated protein system in membrane system. The protein has disulfide bonds. Now I want to simply delete the disulfide bond without disrupting the equilibration. Would you guys suggest easiest way to do that. I know I could use charmm gui but that would alter the positions of lipid, water and ions. Thank you in advance. Have a great summer!!!

Top
#37513 - 05/30/19 03:01 PM Re: delete disulfide bond without alterng membrane protein sysm [Re: Binod]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
Create a patch residue (PRES) which does the opposite of PRES DISU, and apply (command PATCH) it to your PSF. Then generate coordinates for the two missing hydrogens using HBUIld (with no atom-selection).
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Top
#37514 - 05/30/19 03:17 PM Re: delete disulfide bond without alterng membrane protein sysm [Re: Binod]
Binod Offline
Forum Member

Registered: 09/27/16
Posts: 8
Loc: New York, New York
Thank you Lennart for the quick reply, highly appreciated!!

Top
#37515 - 05/31/19 10:26 AM Re: delete disulfide bond without alterng membrane protein sysm [Re: Binod]
Binod Offline
Forum Member

Registered: 09/27/16
Posts: 8
Loc: New York, New York
Hi Lennart,
I have the disulfide bond between resid 6 and 13 in segid PROA. I use the following input file. It ran without the error but the output files still are the same as initial. I am really not that smart on charmm and even reading charmm mannual its still not figure out how to use PRES command. I would greatly appreciate if you modify the following input below





! Read PSF and Coordinates
open read unit 10 card name input.psf
read psf unit 10 card
open read unit 10 card name input.crd
read coor unit 10 card






PRES CYS

HBUIld

open write unit 10 card name final.psf
write psf unit 10 card

open write unit 10 card name final.pdb
write coor unit 10 pdb

open write unit 10 card name final.crd
write coor unit 10 card
close unit 10

stop

Top
#37516 - 05/31/19 12:26 PM Re: delete disulfide bond without alterng membrane protein sysm [Re: Binod]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
Well,
You have to fill in information into PRES CYS, and then read it as an RTF. I amsuprised that you did not get any warnings or errror messages

Something along these lines (see RTF section in io.doc):

Read your parameters, topologies, psf and coordinates. Then

READ RTF CARD APPEND
* patch to break disulfide bond
*
PRES BRDS net charge of the atoms defined in this PRES
ATOM 1CB (fill in information from residue CYS for all these atoms - THIS IS FOR YOU TO DO!!!)
ATOM 1SG
ATOM 1HG1
ATOM 2CB
ATOM 2SG
ATOM 2HG1

BOND 1SG 1HG1
BOND 2SG 2HG1
DELETE BOND 1SG 2SG

END

PATCH BRDS ....
HBUILD


To make life easier for everybody I strongly suggest that you use the format:
read psf card name input.psf
read coor card name input.crd
write coor pdb name final.pdb

instead of the rather OBSOLETE:
open ....
read/write ....
close ...
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Top
#37517 - 05/31/19 02:37 PM Re: delete disulfide bond without alterng membrane protein sysm [Re: Binod]
Binod Offline
Forum Member

Registered: 09/27/16
Posts: 8
Loc: New York, New York
Dear Lennart,
Thank you so much for your help and time. I modified my input file as you suggested. It was my input file, it actually ran and did the patching job. But it gave an error saying missing parameter. I have copied the part of output at the end of the input file.
Thanks
binod


################################################
read psf card name assembly.psf
read coor card name assembly.crd

READ RTF CARD APPEND

!* patch to break disulfide bond
!*

PRES BRDS -0.36 !net charge of the atoms defined in this PRES
ATOM 1CB CT2 -0.11
ATOM 1SG S -0.23
ATOM 1HG1 HS 0.16
ATOM 2CB CT2 -0.11
ATOM 2SG S -0.23
ATOM 2HG1 HS 0.16

BOND 1SG 1HG1
BOND 2SG 2HG1
DELETE BOND 1SG 2SG
END

PATCH BRDS proa 6 proa 15
PATCH BRDS proa 8 proa 13

HBUILD

write psf card name assembly2.psf
write coor card name assembly2.crd
stop
##########################################################





Output file
#############################################################


CHARMM> READ RTF CARD APPEND
MAINIO> Residue topology file being read from unit 5.
RDTITL>
RDTITL> No title read.
WARNING from DECODI -- Zero length string being converted to 0
RTFRDR> WARNING: Version number is NOT specified.

CHARMM>

CHARMM> PATCH BRDS proa 6 proa 15
ATOM PROA CYS 6 HG1 ADDED.
ATOM PROA CYS 15 HG1 ADDED.

Message from MAPIC: Atom numbers are changed.
DELTIC: 1 bonds deleted
AUTOGEN: All angles are removed and regenerated.
AUTOGEN: All dihedrals are removed and regenerated.
: No angle parameters for 541 ( OT HT HT )
: No angle parameters for 542 ( OT HT HT )
: No angle parameters for 544 ( OT HT HT )
: No angle parameters for 545 ( OT HT HT )
: No angle parameters for 547 ( OT HT HT )
: No angle parameters for 548 ( OT HT HT )
: No angle parameters for 550 ( OT HT HT )
: No angle parameters for 551 ( OT HT HT )
: No angle parameters for 553 ( OT HT HT )
: No angle parameters for 554 ( OT HT HT )
: No angle parameters for 556 ( OT HT HT )
: No angle parameters for 557 ( OT HT HT )
: No angle parameters for 559 ( OT HT HT )
: No angle parameters for 560 ( OT HT HT )
: No angle parameters for 562 ( OT HT HT )
: No angle parameters for 563 ( OT HT HT )
: No angle parameters for 565 ( OT HT HT )
: No angle parameters for 566 ( OT HT HT )
: No angle parameters for 568 ( OT HT HT )
: No angle parameters for 569 ( OT HT HT )
: No angle parameters for 571 ( OT HT HT )
: No angle parameters for 572 ( OT HT HT )
: No angle parameters for 574 ( OT HT HT )
: No angle parameters for 575 ( OT HT HT )
: No angle parameters for 577 ( OT HT HT )
: And more missing angle parameters.
: A TOTAL OF 8552 MISSING PARAMETERS

***** LEVEL -1 WARNING FROM *****
***** CODES> MISSING PARAMETERS
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5



/---------\
/ \
/ \
/ \
! XXXX XXXX !
! XXXX XXXX !
! XXX XXX !
! X !
--\ XXX /--
! ! XXX ! !
! ! ! !
! I I I I I !
! I I I I !
\ /
-- --
\---/
XXX XXX
XXXX XXXX
XXXXX XXXXX
XXX XXX
XXX XXX
XXXXX
XXX XXX
XXX XXX
XXX XXX
XXXXX XXXXX
XXXX XXXX
XXX XXX


Execution terminated due to the detection of a fatal error.

************************************************************

Top
#37519 - 06/01/19 01:07 PM Re: delete disulfide bond without alterng membrane protein sysm [Re: Binod]
Binod Offline
Forum Member

Registered: 09/27/16
Posts: 8
Loc: New York, New York
Hello Lennart,
Actually, I tried the input file with the system containing just protein, and it worked fine. But I didn't understand why it didn't work for solvated system.
It seems like in solvated system it didn't find parameters for water even though original psf and crd file were complete and had no missing parameters.
Binod Nepal

Top
#37520 - 06/01/19 04:22 PM Re: delete disulfide bond without alterng membrane protein sysm [Re: Binod]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
The PATCH command automatically generates all possible angles (and dihedrals) in the system, based on the bonded connectivity. Due to the fictitious H-H bond (required for SHAKE) in the TIP3P water model, angles are generated for all waters. Normally when you generate the PSF for waters (which you do last) you explicitly turn off this automatic action for the waters with the keyword NOANGLES to the GENErate command.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Top
#37521 - 06/03/19 08:39 AM Re: delete disulfide bond without alterng membrane protein sysm [Re: Binod]
Binod Offline
Forum Member

Registered: 09/27/16
Posts: 8
Loc: New York, New York
Thank you Lennart. It was the great help for me.
Binod Nepal

Top

Moderator:  alex, chmgr, John Legato