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#37589 - 08/05/19 12:01 PM LYR deprotonation
MD4DW Offline
Forum Member

Registered: 07/10/19
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 !

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#37591 - 08/07/19 04:42 AM Re: LYR deprotonation [Re: MD4DW]
MD4DW Offline
Forum Member

Registered: 07/10/19
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!

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#37592 - 08/07/19 07:01 AM Re: LYR deprotonation [Re: MD4DW]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4755
Loc: ~ 59N, 15E
solvate after you have done the patching.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#37596 - 08/08/19 04:02 AM Re: LYR deprotonation [Re: lennart]
MD4DW Offline
Forum Member

Registered: 07/10/19
Posts: 10
(never mind, solved)


Edited by MD4DW (08/08/19 08:11 AM)

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#37598 - 08/08/19 05:21 AM Re: LYR deprotonation [Re: MD4DW]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4755
Loc: ~ 59N, 15E
when manipulating the PSF there is no need to have periodic boundaries/images present.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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