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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sun Jun 13 2010 - 22:00:03 PDT
