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
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Received on Mon Jun 14 2010 - 00:00:03 PDT
