As you reply to make GL4 7 in the syn-O2 position, change the 2nd value for
resstate to 1.
But I am not getting how to define syn and anti position for O2 (OE2) and O1 (OE1).
Is it on the basis of thier orientation in pdb?
On visualization in pymol GL4 7 is looking like this
3HG 2HE2
\/2HG |
CA CG OE2
/ \ / \ / \
N CB CD 1HE2
\ / \ /
H 2H 3H OE1
/ \
2HE1 1HE1
What is the basis for considering syn and anti for defining protonation state O1
& O2.
I have one more query that when I am making pdb file from prmtop and prmcrd
hydrogen are there.Then when I will modify the protonation state in cpin file,
then what it will do when i will run MD simulation.
Here I am attaching my pdb file which I have created from prmtop prmcrd.
So please give me suggestion.
If you have any refrence about it may I get it from you.
Thanking you
> The resstate is an ordered array. The carboxylates are the 2nd, 5th, 9th,
> 10th, 11th, etc. residues identified in your system. Thus, to make GL4 7
> (the 2nd residue defined for titration, but the 7th residue in the topology
> file) in the syn-O2 position, change the 2nd value for resstate to 1.
>
> Also, I merely suggested that it may be easier to modify resstate in the
> cpin file rather than using the -states flag, since that's what I do.
> However, you can do whatever seems easiest to you.
>
> All the best,
> Jason
>
> On Mon, Jun 14, 2010 at 12:46 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Thanks Jason for reply according to your suggestion I have created cpin
>> file.
>> As you told -states flage should not be specify but I can modify RESSTATE
>> list
>> in cpin file.
>>
>> My cpin hvae folloing RESSTATE descirption:
>>
>> PROTCNT=3,2,0,1,1,1,1,2,1,1,0,1,1,1,1,1,0,
>> RESNAME='System: Unknown','Residue: LYS 1','Residue: GL4 7','Residue: LYS
>> 13',
>> 'Residue: HIP 15','Residue: AS4 18','Residue: TYR 20','Residue: TYR 23',
>> 'Residue: LYS 33','Residue: GL4 35','Residue: AS4 48','Residue: AS4 52',
>> 'Residue: TYR 53','Residue: AS4 66','Residue: AS4 87','Residue: LYS 96',
>> 'Residue: LYS 97','Residue: AS4 101','Residue: LYS 116','Residue: AS4
>> 119',
>> RESSTATE=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,STATEINF(0)%FIRST_ATOM=1,
>> STATEINF(0)%FIRST_CHARGE=0, STATEINF(0)%FIRST_STATE=0,
>> STATEINF(0)%NUM_ATOMS=22, STATEINF(0)%NUM_STATES=2,
>> STATEINF(1)%FIRST_ATOM=103, STATEINF(1)%FIRST_CHARGE=44,
>> STATEINF(1)%FIRST_STATE=2, STATEINF(1)%NUM_ATOMS=19,
>> STATEINF(1)%NUM_STATES=5,
>> STATEINF(2)%FIRST_ATOM=188, STATEINF(2)%FIRST_CHARGE=0,
>> STATEINF(2)%FIRST_STATE=0, STATEINF(2)%NUM_ATOMS=22,
>> STATEINF(2)%NUM_STATES=2,
>> STATEINF(3)%FIRST_ATOM=234, STATEINF(3)%FIRST_CHARGE=139,
>> STATEINF(3)%FIRST_STATE=7, STATEINF(3)%NUM_ATOMS=18,
>> STATEINF(3)%NUM_STATES=3,
>> STATEINF(4)%FIRST_ATOM=278, STATEINF(4)%FIRST_CHARGE=193,
>> STATEINF(4)%FIRST_STATE=10, STATEINF(4)%NUM_ATOMS=16,
>> STATEINF(4)%NUM_STATES=5, STATEINF(5)%FIRST_ATOM=308,
>> STATEINF(5)%FIRST_CHARGE=273, STATEINF(5)%FIRST_STATE=15,
>> STATEINF(5)%NUM_ATOMS=21, STATEINF(5)%NUM_STATES=2,
>> STATEINF(6)%FIRST_ATOM=360, STATEINF(6)%FIRST_CHARGE=273,
>> STATEINF(6)%FIRST_STATE=15, STATEINF(6)%NUM_ATOMS=21,
>> STATEINF(6)%NUM_STATES=2, STATEINF(7)%FIRST_ATOM=503,
>> STATEINF(7)%FIRST_CHARGE=0, STATEINF(7)%FIRST_STATE=0,
>> STATEINF(7)%NUM_ATOMS=22, STATEINF(7)%NUM_STATES=2,
>> STATEINF(8)%FIRST_ATOM=545, STATEINF(8)%FIRST_CHARGE=44,
>> STATEINF(8)%FIRST_STATE=2, STATEINF(8)%NUM_ATOMS=19,
>> STATEINF(8)%NUM_STATES=5,
>> STATEINF(9)%FIRST_ATOM=744, STATEINF(9)%FIRST_CHARGE=193,
>> STATEINF(9)%FIRST_STATE=10, STATEINF(9)%NUM_ATOMS=16,
>> STATEINF(9)%NUM_STATES=5, STATEINF(10)%FIRST_ATOM=792,
>> STATEINF(10)%FIRST_CHARGE=193, STATEINF(10)%FIRST_STATE=10,
>> STATEINF(10)%NUM_ATOMS=16, STATEINF(10)%NUM_STATES=5,
>> STATEINF(11)%FIRST_ATOM=808, STATEINF(11)%FIRST_CHARGE=273,
>> STATEINF(11)%FIRST_STATE=15, STATEINF(11)%NUM_ATOMS=21,
>> STATEINF(11)%NUM_STATES=2, STATEINF(12)%FIRST_ATOM=1032,
>> STATEINF(12)%FIRST_CHARGE=193, STATEINF(12)%FIRST_STATE=10,
>> STATEINF(12)%NUM_ATOMS=16, STATEINF(12)%NUM_STATES=5,
>> STATEINF(13)%FIRST_ATOM=1332, STATEINF(13)%FIRST_CHARGE=193,
>> STATEINF(13)%FIRST_STATE=10, STATEINF(13)%NUM_ATOMS=16,
>> STATEINF(13)%NUM_STATES=5, STATEINF(14)%FIRST_ATOM=1453,
>> STATEINF(14)%FIRST_CHARGE=0, STATEINF(14)%FIRST_STATE=0,
>> STATEINF(14)%NUM_ATOMS=22, STATEINF(14)%NUM_STATES=2,
>> STATEINF(15)%FIRST_ATOM=1475, STATEINF(15)%FIRST_CHARGE=0,
>> STATEINF(15)%FIRST_STATE=0, STATEINF(15)%NUM_ATOMS=22,
>> STATEINF(15)%NUM_STATES=2, STATEINF(16)%FIRST_ATOM=1543,
>> STATEINF(16)%FIRST_CHARGE=193, STATEINF(16)%FIRST_STATE=10,
>> STATEINF(16)%NUM_ATOMS=16, STATEINF(16)%NUM_STATES=5,
>> STATEINF(17)%FIRST_ATOM=1775, STATEINF(17)%FIRST_CHARGE=0,
>> STATEINF(17)%FIRST_STATE=0, STATEINF(17)%NUM_ATOMS=22,
>> STATEINF(17)%NUM_STATES=2, STATEINF(18)%FIRST_ATOM=1818,
>> STATEINF(18)%FIRST_CHARGE=193, STATEINF(18)%FIRST_STATE=10,
>> STATEINF(18)%NUM_ATOMS=16, STATEINF(18)%NUM_STATES=5,
>> STATENE=-0.839279999999999,0,0,14.4775785124894,14.4775785124894,
>> 14.4775785124894,14.4775785124894,0,-11.7817,-16.27078,0,32.288211691664,
>> 32.288211691664,32.288211691664,32.288211691664,0,-78.34438,TRESCNT=19,
>>
>>
>> But I am not getting where to modify it for carboxylate.
>>
>>
>>
>> > Hello,
>> >
>> > In my opinion, you typically don't need to specify the -states flag, as
>> you
>> > can let the states kind of "choose themselves" during your restrained
>> > heating (just make sure that you use the cprestart as the cpin for the
>> > following simulation. The only time you may have to is if, for instance,
>> 2
>> > carboxylates are forming a very tight salt bridge, in which case you may
>> > have to protonate one of them. However, you can just modify the RESSTATE
>> > list in the CPIN file after it's created (you don't have to specify
>> > -states).
>> >
>> > Also, unless you modify CPin.pm, -system does nothing really unless you
>> > specify HEWL (as that is the only system for which experimental pKa data
>> was
>> > put into CPin.pm. However, you can use virtually all flags together
>> (unless
>> > they are mutually exclusive) to create a CPIN file.
>> >
>> > As for the states, different residues have different default states.
>> > Carboxylates have 5 states: deprotonated, and syn or anti on each Oxygen.
>> > It just so happens that state 0 is deprotonated, 1 is syn on O2, 2 is
>> anti
>> > on O2, 3 is syn on O1, and 4 is anti on O1. Histidine, state 0 is HIP, 1
>> is
>> > HID, and 2 is HIE (3 states total). All of these are commented at the
>> > bottom of the CPin.pm file, I can't remember if they're explicitly stated
>> in
>> > the manual.
>> >
>> > Hope this helps,
>> > Jason
>> >
>> > On Sun, Jun 13, 2010 at 12:16 PM, Sangita Kachhap <sangita.imtech.res.in
>> >wrote:
>> >
>> >>
>> >> Hello all
>> >>
>> >> I am doing constant pH simulation at pH 4 .Should I specify the -states
>> >> flag for
>> >> generation of cpin file?
>> >>
>> >> In manual by default protonation state is 0: which specify
>> >> deprotonated for ASP and GLU, protonated for LYS and TYR, doubly
>> protonated
>> >> for
>> >> HIS (i.e. HIP).
>> >>
>> >> In example there is other protonation state 1, 3:
>> >>
>> >> ambpdb -p prmtop < prmcrd | cpinutil.pl -states 1,3,0,0,0,1 > cpin
>> >>
>> >> So what is mean by protonation state 1, 3
>> >>
>> >> Can I specify both -state & -system flag during generation of cpin file?
>> >>
>> >> Seeking for suggestion.
>> >>
>> >> With regard
>> >> Sangita Kachhap
>> >> JRF
>> >> BIC,IMTECH
>> >> CHANDIGARH
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>> >
>> > --
>> > Jason M. Swails
>> > Quantum Theory Project,
>> > University of Florida
>> > Ph.D. Graduate Student
>> > 352-392-4032
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>>
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Tue Jun 15 2010 - 07:00:04 PDT
