Previous Thread
Next Thread
Print Thread
LYR deprotonation
#37589 08/05/19 04:01 PM
Joined: Jul 2019
Posts: 10
M
MD4DW Offline OP
Forum Member
OP Offline
Forum Member
M
Joined: Jul 2019
Posts: 10
Hey there dear CHARMM experts, I hope you could help me with the following problem:
I am a bit confused as to what will be the best way for me to convert a LYR (protonated Schiff-base retinal) in my structure to a deprotonated schiff-base retinal. The patch SCK0 seem to need the lysin and retinal as separate entities and there is no residue in the prot_retinol file that matches what I need.
What would be the best way to go about this?

Thank you in advance !

Re: LYR deprotonation
MD4DW #37591 08/07/19 08:42 AM
Joined: Jul 2019
Posts: 10
M
MD4DW Offline OP
Forum Member
OP Offline
Forum Member
M
Joined: Jul 2019
Posts: 10
Update: I have decided to customize SCK0 to work with LYR as rest to be patched:
++++++++++++++++++++++++++++++++++++++++++++++++++
PRES PLYR 0.00 ! patch to form a
! deprotonated schiff's base from LYR
! follow with AUTOgenerate ANGLes DIHEdrals command
DELETE ATOM HZ1

GROUP ! HE1(HE2) HE2(HE3)
ATOM CE CT2 0.04 ! \ /
ATOM HE2 HA2 0.09 ! --1CE1(CE) 2H15(H11)
ATOM HE3 HA2 0.09 ! \ /
ATOM NZ NS1 -0.60 ! 1NZ(NZ)=2C15(C1)
ATOM C1 CC1B 0.23 ! / \
ATOM H11 HE1 0.15 ! 2HZ1(HZ1) 2C14(C2)==
GROUP ! /
ATOM C2 CC1A -0.15 ! 2HE14(HC2)
ATOM HC2 HE1 0.15
++++++++++++++++++++++++++++++++++++++++++++++++++++

My problem now is that when the proton gets deleted, an AUTOGEN seems to run automatically, thereby making a problem with the water (TIP3) in my structure:

+++++++++++++++++++++++++++++++++++++++++++++++++++

CHARMM> !
CHARMM> ! patchwork
CHARMM> !
CHARMM> patch PLYR PROA 255
ATOM PROA 255 LYR HZ1 AND ALL REFERENCES TO IT DELETED.

Message from MAPIC: Atom numbers are changed.
DELTIC: 1 bonds deleted
DELTIC: 2 angles deleted
DELTIC: 5 dihedrals deleted
DELTIC: 1 donors deleted
AUTOGEN: All angles are removed and regenerated.
AUTOGEN: All dihedrals are removed and regenerated.
: No angle parameters for 42053 ( OT HT HT )
: No angle parameters for 42054 ( OT HT HT )
: No angle parameters for 42056 ( OT HT HT )
: No angle parameters for 42057 ( OT HT HT )
: No angle parameters for 42059 ( OT HT HT )
: No angle parameters for 42060 ( OT HT HT )
: No angle parameters for 42062 ( OT HT HT )
: No angle parameters for 42063 ( OT HT HT )
: No angle parameters for 42065 ( OT HT HT )
: No angle parameters for 42066 ( OT HT HT )
: No angle parameters for 42068 ( OT HT HT )
: No angle parameters for 42069 ( OT HT HT )
: No angle parameters for 42071 ( OT HT HT )
: No angle parameters for 42072 ( OT HT HT )
: No angle parameters for 42074 ( OT HT HT )
: No angle parameters for 42075 ( OT HT HT )
: No angle parameters for 42077 ( OT HT HT )
: No angle parameters for 42078 ( OT HT HT )
: No angle parameters for 42080 ( OT HT HT )
: No angle parameters for 42081 ( OT HT HT )
: No angle parameters for 42083 ( OT HT HT )
: No angle parameters for 42084 ( OT HT HT )
: No angle parameters for 42086 ( OT HT HT )
: No angle parameters for 42087 ( OT HT HT )
: No angle parameters for 42089 ( OT HT HT )
: And more missing angle parameters.
: A TOTAL OF28302 MISSING PARAMETERS

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


+++++++++++++++++++++++++++++++++++++++++++++++++++

Any tips for handling this problem?

Thanks!

Re: LYR deprotonation
MD4DW #37592 08/07/19 11:01 AM
Joined: Sep 2003
Posts: 4,777
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,777
Likes: 2
solvate after you have done the patching.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: LYR deprotonation
lennart #37596 08/08/19 08:02 AM
Joined: Jul 2019
Posts: 10
M
MD4DW Offline OP
Forum Member
OP Offline
Forum Member
M
Joined: Jul 2019
Posts: 10
(never mind, solved)

Last edited by MD4DW; 08/08/19 12:11 PM.
Re: LYR deprotonation
MD4DW #37598 08/08/19 09:21 AM
Joined: Sep 2003
Posts: 4,777
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,777
Likes: 2
when manipulating the PSF there is no need to have periodic boundaries/images present.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.013s Queries: 24 (0.006s) Memory: 0.9248 MB (Peak: 1.0175 MB) Data Comp: Off Server Time: 2020-07-08 02:33:01 UTC
Valid HTML 5 and Valid CSS