am I reading correctly that you are trying to titrate > 80 residues at
the same time ?
I believe we set
constantph.F90:#define MAX_TITR_RES 50
So this would not work.
However, I am puzzled by the error message you are getting, it should
tell you that your number of residues is > MAX_TITR_RES and not, like
you have, report a namelist error.
Can you do me a favor ?
Try titrating a MUCH smaller number of residues, perhaps 40 or so, let's
see if that works.
If that works, then you need to go into your constantph.F90 file, change
MAX_TITR_RES and recompiple.
Now, that is an EXPERT setting. Unless you are sure of what you are
doing, I strongly reccomend against changing it.
One a more science-related note, it is extremely unlikely that you ever
really need to titrate THAT many residues.
For most systems, the assumption that a lysine and a cysteine for
instance are protonated for pH < 8 or 9 is is a good one. Same for
ASP/GLU, that should be deprotonated at ph=9, which is what your input says.
So, unless you are suspecting your system to be strange, the chances
that you need to titrate ASP and LYS and the same time are really slim.
There are plenty of interesting systems where this is needed, but you
need to really lokk into your own system and decide.
adrian
On 3/8/17 4:41 AM, EGIDEA PUTI DEVINA wrote:
> Hi
>
> Here's the cpin file
>
> &CNSTPH
> CHRGDAT=-0.4157,0.2719,0.0341,0.0864,-0.1783,-0.0122,-
> 0.0122,0.7994,-0.8014,
> -0.8014,0.0,0.5973,-0.5679,0.0,0.0,0.0,-0.4157,0.2719,0.
> 0341,0.0864,-0.0316,
> 0.0488,0.0488,0.6462,-0.5554,-0.6376,0.4747,0.5973,-0.5679,
> 0.0,0.0,0.0,-0.4157,
> 0.2719,0.0341,0.0864,-0.0316,0.0488,0.0488,0.6462,-0.5554,-
> 0.6376,0.0,0.5973,
> -0.5679,0.4747,0.0,0.0,-0.4157,0.2719,0.0341,0.0864,-0.0316,0.0488,0.0488,
> 0.6462,-0.6376,-0.5554,0.0,0.5973,-0.5679,0.0,0.4747,0.0,-
> 0.4157,0.2719,0.0341,
> 0.0864,-0.0316,0.0488,0.0488,0.6462,-0.6376,-0.5554,0.0,0.
> 5973,-0.5679,0.0,0.0,
> 0.4747,-0.3479,0.2747,-0.1354,0.1212,-0.0414,0.081,0.081,-0.0012,-0.1513,
> 0.3866,-0.017,0.2681,-0.1718,0.3911,-0.1141,0.2317,0.7341,-0.5894,-0.3479,
> 0.2747,-0.1354,0.1212,-0.111,0.0402,0.0402,-0.0266,-0.3811,0.3649,0.2057,
> 0.1392,-0.5727,0.0,0.1292,0.1147,0.7341,-0.5894,-0.3479,0.
> 2747,-0.1354,0.1212,
> -0.1012,0.0367,0.0367,0.1868,-0.5432,0.0,0.1635,0.1435,-0.
> 2795,0.3339,-0.2207,
> 0.1862,0.7341,-0.5894,-0.4157,0.2719,0.0145,0.0779,-0.0398,-0.0173,-0.0173,
> 0.0136,-0.0425,-0.0425,0.8054,-0.8188,-0.8188,0.0,0.
> 5973,-0.5679,0.0,0.0,0.0,
> -0.4157,0.2719,0.0145,0.0779,-0.0071,0.0256,0.0256,-0.0174,
> 0.043,0.043,0.6801,
> -0.5838,-0.6511,0.4641,0.5973,-0.5679,0.0,0.0,0.0,-0.
> 4157,0.2719,0.0145,0.0779,
> -0.0071,0.0256,0.0256,-0.0174,0.043,0.043,0.6801,-0.
> 5838,-0.6511,0.0,0.5973,
> -0.5679,0.4641,0.0,0.0,-0.4157,0.2719,0.0145,0.0779,-0.0071,0.0256,0.0256,
> -0.0174,0.043,0.043,0.6801,-0.6511,-0.5838,0.0,0.5973,-0.
> 5679,0.0,0.4641,0.0,
> -0.4157,0.2719,0.0145,0.0779,-0.0071,0.0256,0.0256,-0.0174,
> 0.043,0.043,0.6801,
> -0.6511,-0.5838,0.0,0.5973,-0.5679,0.0,0.0,0.4641,-0.3479,
> 0.2747,-0.24,0.1426,
> -0.0094,0.0362,0.0362,0.0187,0.0103,0.0103,-0.0479,0.0621,0.0621,-0.0143,
> 0.1135,0.1135,-0.3854,0.34,0.34,0.34,0.7341,-0.5894,-0.3479,0.2747,-0.24,
> 0.1426,-0.10961,0.034,0.034,0.06612,0.01041,0.01041,-0.
> 03768,0.01155,0.01155,
> 0.32604,-0.03358,-0.03358,-1.03581,0.0,0.38604,0.38604,0.
> 7341,-0.5894,-0.4157,
> 0.2719,-0.0014,0.0876,-0.0152,0.0295,0.0295,-0.0011,-0.1906,0.1699,-0.2341,
> 0.1656,0.3226,-0.5579,0.3992,-0.2341,0.1656,-0.1906,0.1699,0.5973,-0.5679,
> -0.4157,0.2719,-0.0014,0.0876,-0.0858,0.019,0.019,-0.
> 213,-0.103,0.132,-0.498,
> 0.132,0.777,-0.814,0.0,-0.498,0.132,-0.103,0.132,0.5973,
> -0.5679,-0.4157,0.2719,
> 0.0213,0.1124,-0.1231,0.1112,0.1112,-0.3119,0.1933,0.5973,-0.5679,-0.4157,
> 0.2719,0.0213,0.1124,-0.3593,0.1122,0.1122,-0.8844,0.0,0.5973,-0.5679,
> PROTCNT=0,1,1,1,1,2,1,1,0,1,1,1,1,3,2,1,0,1,0,
> RESNAME='System: Unknown','Residue: AS4 7','Residue: HIP 14','Residue: GL4
> 22',
> 'Residue: GL4 23','Residue: LYS 28','Residue: TYR 29','Residue: AS4 36',
> 'Residue: GL4 38','Residue: AS4 43','Residue: TYR 46','Residue: TYR 49',
> 'Residue: AS4 61','Residue: CYS 64','Residue: GL4 65','Residue: TYR 67',
> 'Residue: AS4 76','Residue: TYR 77','Residue: HIP 81','Residue: LYS 84',
> 'Residue: HIP 85','Residue: HIP 87','Residue: TYR 94','Residue: GL4 100',
> 'Residue: LYS 102','Residue: HIP 108','Residue: HIP 112','Residue: GL4
> 127',
> 'Residue: GL4 132','Residue: GL4 133','Residue: GL4 135','Residue: TYR
> 136',
> 'Residue: GL4 138','Residue: HIP 140','Residue: GL4 149','Residue: HIP
> 152',
> 'Residue: HIP 153','Residue: HIP 165','Residue: AS4 166','Residue: AS4
> 175',
> 'Residue: AS4 178','Residue: AS4 182','Residue: LYS 185','Residue: GL4
> 189',
> 'Residue: TYR 199','Residue: TYR 204','Residue: AS4 205','Residue: LYS
> 207',
> 'Residue: AS4 209','Residue: GL4 219','Residue: AS4 222','Residue: HIP
> 223',
> 'Residue: TYR 224','Residue: GL4 226','Residue: LYS 229','Residue: AS4
> 238',
> 'Residue: TYR 242','Residue: AS4 243','Residue: GL4 250','Residue: LYS
> 251',
> 'Residue: TYR 263','Residue: TYR 264','Residue: GL4 270','Residue: TYR
> 273',
> 'Residue: TYR 281','Residue: TYR 282','Residue: GL4 284','Residue: CYS
> 295',
> 'Residue: TYR 302','Residue: AS4 310','Residue: AS4 311','Residue: GL4
> 315',
> 'Residue: AS4 317','Residue: LYS 329','Residue: AS4 334','Residue: TYR
> 339',
> 'Residue: AS4 340','Residue: LYS 344','Residue: LYS 345','Residue: AS4
> 350',
> 'Residue: TYR 354','Residue: AS4 357','Residue: HIP 358','Residue: GL4
> 360',
> 'Residue: AS4 365','Residue: AS4 371','Residue: TYR 376','Residue: GL4
> 381',
> RESSTATE=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,0,0,0,0,0,
> STATEINF(0)%FIRST_ATOM=88, STATEINF(0)%FIRST_CHARGE=0,
> STATEINF(0)%FIRST_STATE=0, STATEINF(0)%NUM_ATOMS=16,
> STATEINF(0)%NUM_STATES=5,
> STATEINF(1)%FIRST_ATOM=201, STATEINF(1)%FIRST_CHARGE=80,
> STATEINF(1)%FIRST_STATE=5, STATEINF(1)%NUM_ATOMS=18,
> STATEINF(1)%NUM_STATES=3,
> STATEINF(2)%FIRST_ATOM=322, STATEINF(2)%FIRST_CHARGE=134,
> STATEINF(2)%FIRST_STATE=8, STATEINF(2)%NUM_ATOMS=19,
> STATEINF(2)%NUM_STATES=5,
> STATEINF(3)%FIRST_ATOM=341, STATEINF(3)%FIRST_CHARGE=134,
> STATEINF(3)%FIRST_STATE=8, STATEINF(3)%NUM_ATOMS=19,
> STATEINF(3)%NUM_STATES=5,
> STATEINF(4)%FIRST_ATOM=424, STATEINF(4)%FIRST_CHARGE=229,
> STATEINF(4)%FIRST_STATE=13, STATEINF(4)%NUM_ATOMS=22,
> STATEINF(4)%NUM_STATES=2, STATEINF(5)%FIRST_ATOM=446,
> STATEINF(5)%FIRST_CHARGE=273, STATEINF(5)%FIRST_STATE=15,
> STATEINF(5)%NUM_ATOMS=21, STATEINF(5)%NUM_STATES=2,
> STATEINF(6)%FIRST_ATOM=552, STATEINF(6)%FIRST_CHARGE=0,
> STATEINF(6)%FIRST_STATE=0, STATEINF(6)%NUM_ATOMS=16,
> STATEINF(6)%NUM_STATES=5,
> STATEINF(7)%FIRST_ATOM=587, STATEINF(7)%FIRST_CHARGE=134,
> STATEINF(7)%FIRST_STATE=8, STATEINF(7)%NUM_ATOMS=19,
> STATEINF(7)%NUM_STATES=5,
> STATEINF(8)%FIRST_ATOM=680, STATEINF(8)%FIRST_CHARGE=0,
> STATEINF(8)%FIRST_STATE=0, STATEINF(8)%NUM_ATOMS=16,
> STATEINF(8)%NUM_STATES=5,
> STATEINF(9)%FIRST_ATOM=717, STATEINF(9)%FIRST_CHARGE=273,
> STATEINF(9)%FIRST_STATE=15, STATEINF(9)%NUM_ATOMS=21,
> STATEINF(9)%NUM_STATES=2, STATEINF(10)%FIRST_ATOM=776,
> STATEINF(10)%FIRST_CHARGE=273, STATEINF(10)%FIRST_STATE=15,
> STATEINF(10)%NUM_ATOMS=21, STATEINF(10)%NUM_STATES=2,
> STATEINF(11)%FIRST_ATOM=956, STATEINF(11)%FIRST_CHARGE=0,
> STATEINF(11)%FIRST_STATE=0, STATEINF(11)%NUM_ATOMS=16,
> STATEINF(11)%NUM_STATES=5, STATEINF(12)%FIRST_ATOM=1006,
> STATEINF(12)%FIRST_CHARGE=315, STATEINF(12)%FIRST_STATE=17,
> STATEINF(12)%NUM_ATOMS=11, STATEINF(12)%NUM_STATES=2,
> STATEINF(13)%FIRST_ATOM=1017, STATEINF(13)%FIRST_CHARGE=134,
> STATEINF(13)%FIRST_STATE=8, STATEINF(13)%NUM_ATOMS=19,
> STATEINF(13)%NUM_STATES=5, STATEINF(14)%FIRST_ATOM=1046,
> STATEINF(14)%FIRST_CHARGE=273, STATEINF(14)%FIRST_STATE=15,
> STATEINF(14)%NUM_ATOMS=21, STATEINF(14)%NUM_STATES=2,
> STATEINF(15)%FIRST_ATOM=1173, STATEINF(15)%FIRST_CHARGE=0,
> STATEINF(15)%FIRST_STATE=0, STATEINF(15)%NUM_ATOMS=16,
> STATEINF(15)%NUM_STATES=5, STATEINF(16)%FIRST_ATOM=1189,
> STATEINF(16)%FIRST_CHARGE=273, STATEINF(16)%FIRST_STATE=15,
> STATEINF(16)%NUM_ATOMS=21, STATEINF(16)%NUM_STATES=2,
> STATEINF(17)%FIRST_ATOM=1237, STATEINF(17)%FIRST_CHARGE=80,
> STATEINF(17)%FIRST_STATE=5, STATEINF(17)%NUM_ATOMS=18,
> STATEINF(17)%NUM_STATES=3, STATEINF(18)%FIRST_ATOM=1275,
> STATEINF(18)%FIRST_CHARGE=229, STATEINF(18)%FIRST_STATE=13,
> STATEINF(18)%NUM_ATOMS=22, STATEINF(18)%NUM_STATES=2,
> STATEINF(19)%FIRST_ATOM=1297, STATEINF(19)%FIRST_CHARGE=80,
> STATEINF(19)%FIRST_STATE=5, STATEINF(19)%NUM_ATOMS=18,
> STATEINF(19)%NUM_STATES=3, STATEINF(20)%FIRST_ATOM=1322,
> STATEINF(20)%FIRST_CHARGE=80, STATEINF(20)%FIRST_STATE=5,
> STATEINF(20)%NUM_ATOMS=18, STATEINF(20)%NUM_STATES=3,
> STATEINF(21)%FIRST_ATOM=1439, STATEINF(21)%FIRST_CHARGE=273,
> STATEINF(21)%FIRST_STATE=15, STATEINF(21)%NUM_ATOMS=21,
> STATEINF(21)%NUM_STATES=2, STATEINF(22)%FIRST_ATOM=1533,
> STATEINF(22)%FIRST_CHARGE=134, STATEINF(22)%FIRST_STATE=8,
> STATEINF(22)%NUM_ATOMS=19, STATEINF(22)%NUM_STATES=5,
> STATEINF(23)%FIRST_ATOM=1571, STATEINF(23)%FIRST_CHARGE=229,
> STATEINF(23)%FIRST_STATE=13, STATEINF(23)%NUM_ATOMS=22,
> STATEINF(23)%NUM_STATES=2, STATEINF(24)%FIRST_ATOM=1674,
> STATEINF(24)%FIRST_CHARGE=80, STATEINF(24)%FIRST_STATE=5,
> STATEINF(24)%NUM_ATOMS=18, STATEINF(24)%NUM_STATES=3,
> STATEINF(25)%FIRST_ATOM=1740, STATEINF(25)%FIRST_CHARGE=80,
> STATEINF(25)%FIRST_STATE=5, STATEINF(25)%NUM_ATOMS=18,
> STATEINF(25)%NUM_STATES=3, STATEINF(26)%FIRST_ATOM=1966,
> STATEINF(26)%FIRST_CHARGE=134, STATEINF(26)%FIRST_STATE=8,
> STATEINF(26)%NUM_ATOMS=19, STATEINF(26)%NUM_STATES=5,
> STATEINF(27)%FIRST_ATOM=2034, STATEINF(27)%FIRST_CHARGE=134,
> STATEINF(27)%FIRST_STATE=8, STATEINF(27)%NUM_ATOMS=19,
> STATEINF(27)%NUM_STATES=5, STATEINF(28)%FIRST_ATOM=2053,
> STATEINF(28)%FIRST_CHARGE=134, STATEINF(28)%FIRST_STATE=8,
> STATEINF(28)%NUM_ATOMS=19, STATEINF(28)%NUM_STATES=5,
> STATEINF(29)%FIRST_ATOM=2096, STATEINF(29)%FIRST_CHARGE=134,
> STATEINF(29)%FIRST_STATE=8, STATEINF(29)%NUM_ATOMS=19,
> STATEINF(29)%NUM_STATES=5, STATEINF(30)%FIRST_ATOM=2115,
> STATEINF(30)%FIRST_CHARGE=273, STATEINF(30)%FIRST_STATE=15,
> STATEINF(30)%NUM_ATOMS=21, STATEINF(30)%NUM_STATES=2,
> STATEINF(31)%FIRST_ATOM=2146, STATEINF(31)%FIRST_CHARGE=134,
> STATEINF(31)%FIRST_STATE=8, STATEINF(31)%NUM_ATOMS=19,
> STATEINF(31)%NUM_STATES=5, STATEINF(32)%FIRST_ATOM=2175,
> STATEINF(32)%FIRST_CHARGE=80, STATEINF(32)%FIRST_STATE=5,
> STATEINF(32)%NUM_ATOMS=18, STATEINF(32)%NUM_STATES=3,
> STATEINF(33)%FIRST_ATOM=2317, STATEINF(33)%FIRST_CHARGE=134,
> STATEINF(33)%FIRST_STATE=8, STATEINF(33)%NUM_ATOMS=19,
> STATEINF(33)%NUM_STATES=5, STATEINF(34)%FIRST_ATOM=2350,
> STATEINF(34)%FIRST_CHARGE=80, STATEINF(34)%FIRST_STATE=5,
> STATEINF(34)%NUM_ATOMS=18, STATEINF(34)%NUM_STATES=3,
> STATEINF(35)%FIRST_ATOM=2368, STATEINF(35)%FIRST_CHARGE=80,
> STATEINF(35)%FIRST_STATE=5, STATEINF(35)%NUM_ATOMS=18,
> STATEINF(35)%NUM_STATES=3, STATEINF(36)%FIRST_ATOM=2547,
> STATEINF(36)%FIRST_CHARGE=80, STATEINF(36)%FIRST_STATE=5,
> STATEINF(36)%NUM_ATOMS=18, STATEINF(36)%NUM_STATES=3,
> STATEINF(37)%FIRST_ATOM=2565, STATEINF(37)%FIRST_CHARGE=0,
> STATEINF(37)%FIRST_STATE=0, STATEINF(37)%NUM_ATOMS=16,
> STATEINF(37)%NUM_STATES=5, STATEINF(38)%FIRST_ATOM=2698,
> STATEINF(38)%FIRST_CHARGE=0, STATEINF(38)%FIRST_STATE=0,
> STATEINF(38)%NUM_ATOMS=16, STATEINF(38)%NUM_STATES=5,
> STATEINF(39)%FIRST_ATOM=2748, STATEINF(39)%FIRST_CHARGE=0,
> STATEINF(39)%FIRST_STATE=0, STATEINF(39)%NUM_ATOMS=16,
> STATEINF(39)%NUM_STATES=5, STATEINF(40)%FIRST_ATOM=2828,
> STATEINF(40)%FIRST_CHARGE=0, STATEINF(40)%FIRST_STATE=0,
> STATEINF(40)%NUM_ATOMS=16, STATEINF(40)%NUM_STATES=5,
> STATEINF(41)%FIRST_ATOM=2880, STATEINF(41)%FIRST_CHARGE=229,
> STATEINF(41)%FIRST_STATE=13, STATEINF(41)%NUM_ATOMS=22,
> STATEINF(41)%NUM_STATES=2, STATEINF(42)%FIRST_ATOM=2947,
> STATEINF(42)%FIRST_CHARGE=134, STATEINF(42)%FIRST_STATE=8,
> STATEINF(42)%NUM_ATOMS=19, STATEINF(42)%NUM_STATES=5,
> STATEINF(43)%FIRST_ATOM=3077, STATEINF(43)%FIRST_CHARGE=273,
> STATEINF(43)%FIRST_STATE=15, STATEINF(43)%NUM_ATOMS=21,
> STATEINF(43)%NUM_STATES=2, STATEINF(44)%FIRST_ATOM=3156,
> STATEINF(44)%FIRST_CHARGE=273, STATEINF(44)%FIRST_STATE=15,
> STATEINF(44)%NUM_ATOMS=21, STATEINF(44)%NUM_STATES=2,
> STATEINF(45)%FIRST_ATOM=3177, STATEINF(45)%FIRST_CHARGE=0,
> STATEINF(45)%FIRST_STATE=0, STATEINF(45)%NUM_ATOMS=16,
> STATEINF(45)%NUM_STATES=5, STATEINF(46)%FIRST_ATOM=3213,
> STATEINF(46)%FIRST_CHARGE=229, STATEINF(46)%FIRST_STATE=13,
> STATEINF(46)%NUM_ATOMS=22, STATEINF(46)%NUM_STATES=2,
> STATEINF(47)%FIRST_ATOM=3254, STATEINF(47)%FIRST_CHARGE=0,
> STATEINF(47)%FIRST_STATE=0, STATEINF(47)%NUM_ATOMS=16,
> STATEINF(47)%NUM_STATES=5, STATEINF(48)%FIRST_ATOM=3423,
> STATEINF(48)%FIRST_CHARGE=134, STATEINF(48)%FIRST_STATE=8,
> STATEINF(48)%NUM_ATOMS=19, STATEINF(48)%NUM_STATES=5,
> STATEINF(49)%FIRST_ATOM=3473, STATEINF(49)%FIRST_CHARGE=0,
> STATEINF(49)%FIRST_STATE=0, STATEINF(49)%NUM_ATOMS=16,
> STATEINF(49)%NUM_STATES=5, STATEINF(50)%FIRST_ATOM=3489,
> STATEINF(50)%FIRST_CHARGE=80, STATEINF(50)%FIRST_STATE=5,
> STATEINF(50)%NUM_ATOMS=18, STATEINF(50)%NUM_STATES=3,
> STATEINF(51)%FIRST_ATOM=3507, STATEINF(51)%FIRST_CHARGE=273,
> STATEINF(51)%FIRST_STATE=15, STATEINF(51)%NUM_ATOMS=21,
> STATEINF(51)%NUM_STATES=2, STATEINF(52)%FIRST_ATOM=3548,
> STATEINF(52)%FIRST_CHARGE=134, STATEINF(52)%FIRST_STATE=8,
> STATEINF(52)%NUM_ATOMS=19, STATEINF(52)%NUM_STATES=5,
> STATEINF(53)%FIRST_ATOM=3610, STATEINF(53)%FIRST_CHARGE=229,
> STATEINF(53)%FIRST_STATE=13, STATEINF(53)%NUM_ATOMS=22,
> STATEINF(53)%NUM_STATES=2, STATEINF(54)%FIRST_ATOM=3760,
> STATEINF(54)%FIRST_CHARGE=0, STATEINF(54)%FIRST_STATE=0,
> STATEINF(54)%NUM_ATOMS=16, STATEINF(54)%NUM_STATES=5,
> STATEINF(55)%FIRST_ATOM=3824, STATEINF(55)%FIRST_CHARGE=273,
> STATEINF(55)%FIRST_STATE=15, STATEINF(55)%NUM_ATOMS=21,
> STATEINF(55)%NUM_STATES=2, STATEINF(56)%FIRST_ATOM=3845,
> STATEINF(56)%FIRST_CHARGE=0, STATEINF(56)%FIRST_STATE=0,
> STATEINF(56)%NUM_ATOMS=16, STATEINF(56)%NUM_STATES=5,
> STATEINF(57)%FIRST_ATOM=3935, STATEINF(57)%FIRST_CHARGE=134,
> STATEINF(57)%FIRST_STATE=8, STATEINF(57)%NUM_ATOMS=19,
> STATEINF(57)%NUM_STATES=5, STATEINF(58)%FIRST_ATOM=3954,
> STATEINF(58)%FIRST_CHARGE=229, STATEINF(58)%FIRST_STATE=13,
> STATEINF(58)%NUM_ATOMS=22, STATEINF(58)%NUM_STATES=2,
> STATEINF(59)%FIRST_ATOM=4146, STATEINF(59)%FIRST_CHARGE=273,
> STATEINF(59)%FIRST_STATE=15, STATEINF(59)%NUM_ATOMS=21,
> STATEINF(59)%NUM_STATES=2, STATEINF(60)%FIRST_ATOM=4167,
> STATEINF(60)%FIRST_CHARGE=273, STATEINF(60)%FIRST_STATE=15,
> STATEINF(60)%NUM_ATOMS=21, STATEINF(60)%NUM_STATES=2,
> STATEINF(61)%FIRST_ATOM=4262, STATEINF(61)%FIRST_CHARGE=134,
> STATEINF(61)%FIRST_STATE=8, STATEINF(61)%NUM_ATOMS=19,
> STATEINF(61)%NUM_STATES=5, STATEINF(62)%FIRST_ATOM=4319,
> STATEINF(62)%FIRST_CHARGE=273, STATEINF(62)%FIRST_STATE=15,
> STATEINF(62)%NUM_ATOMS=21, STATEINF(62)%NUM_STATES=2,
> STATEINF(63)%FIRST_ATOM=4435, STATEINF(63)%FIRST_CHARGE=273,
> STATEINF(63)%FIRST_STATE=15, STATEINF(63)%NUM_ATOMS=21,
> STATEINF(63)%NUM_STATES=2, STATEINF(64)%FIRST_ATOM=4456,
> STATEINF(64)%FIRST_CHARGE=273, STATEINF(64)%FIRST_STATE=15,
> STATEINF(64)%NUM_ATOMS=21, STATEINF(64)%NUM_STATES=2,
> STATEINF(65)%FIRST_ATOM=4491, STATEINF(65)%FIRST_CHARGE=134,
> STATEINF(65)%FIRST_STATE=8, STATEINF(65)%NUM_ATOMS=19,
> STATEINF(65)%NUM_STATES=5, STATEINF(66)%FIRST_ATOM=4650,
> STATEINF(66)%FIRST_CHARGE=315, STATEINF(66)%FIRST_STATE=17,
> STATEINF(66)%NUM_ATOMS=11, STATEINF(66)%NUM_STATES=2,
> STATEINF(67)%FIRST_ATOM=4742, STATEINF(67)%FIRST_CHARGE=273,
> STATEINF(67)%FIRST_STATE=15, STATEINF(67)%NUM_ATOMS=21,
> STATEINF(67)%NUM_STATES=2, STATEINF(68)%FIRST_ATOM=4874,
> STATEINF(68)%FIRST_CHARGE=0, STATEINF(68)%FIRST_STATE=0,
> STATEINF(68)%NUM_ATOMS=16, STATEINF(68)%NUM_STATES=5,
> STATEINF(69)%FIRST_ATOM=4890, STATEINF(69)%FIRST_CHARGE=0,
> STATEINF(69)%FIRST_STATE=0, STATEINF(69)%NUM_ATOMS=16,
> STATEINF(69)%NUM_STATES=5, STATEINF(70)%FIRST_ATOM=4973,
> STATEINF(70)%FIRST_CHARGE=134, STATEINF(70)%FIRST_STATE=8,
> STATEINF(70)%NUM_ATOMS=19, STATEINF(70)%NUM_STATES=5,
> STATEINF(71)%FIRST_ATOM=5006, STATEINF(71)%FIRST_CHARGE=0,
> STATEINF(71)%FIRST_STATE=0, STATEINF(71)%NUM_ATOMS=16,
> STATEINF(71)%NUM_STATES=5, STATEINF(72)%FIRST_ATOM=5171,
> STATEINF(72)%FIRST_CHARGE=229, STATEINF(72)%FIRST_STATE=13,
> STATEINF(72)%NUM_ATOMS=22, STATEINF(72)%NUM_STATES=2,
> STATEINF(73)%FIRST_ATOM=5246, STATEINF(73)%FIRST_CHARGE=0,
> STATEINF(73)%FIRST_STATE=0, STATEINF(73)%NUM_ATOMS=16,
> STATEINF(73)%NUM_STATES=5, STATEINF(74)%FIRST_ATOM=5335,
> STATEINF(74)%FIRST_CHARGE=273, STATEINF(74)%FIRST_STATE=15,
> STATEINF(74)%NUM_ATOMS=21, STATEINF(74)%NUM_STATES=2,
> STATEINF(75)%FIRST_ATOM=5356, STATEINF(75)%FIRST_CHARGE=0,
> STATEINF(75)%FIRST_STATE=0, STATEINF(75)%NUM_ATOMS=16,
> STATEINF(75)%NUM_STATES=5, STATEINF(76)%FIRST_ATOM=5408,
> STATEINF(76)%FIRST_CHARGE=229, STATEINF(76)%FIRST_STATE=13,
> STATEINF(76)%NUM_ATOMS=22, STATEINF(76)%NUM_STATES=2,
> STATEINF(77)%FIRST_ATOM=5430, STATEINF(77)%FIRST_CHARGE=229,
> STATEINF(77)%FIRST_STATE=13, STATEINF(77)%NUM_ATOMS=22,
> STATEINF(77)%NUM_STATES=2, STATEINF(78)%FIRST_ATOM=5513,
> STATEINF(78)%FIRST_CHARGE=0, STATEINF(78)%FIRST_STATE=0,
> STATEINF(78)%NUM_ATOMS=16, STATEINF(78)%NUM_STATES=5,
> STATEINF(79)%FIRST_ATOM=5567, STATEINF(79)%FIRST_CHARGE=273,
> STATEINF(79)%FIRST_STATE=15, STATEINF(79)%NUM_ATOMS=21,
> STATEINF(79)%NUM_STATES=2, STATEINF(80)%FIRST_ATOM=5618,
> STATEINF(80)%FIRST_CHARGE=0, STATEINF(80)%FIRST_STATE=0,
> STATEINF(80)%NUM_ATOMS=16, STATEINF(80)%NUM_STATES=5,
> STATEINF(81)%FIRST_ATOM=5634, STATEINF(81)%FIRST_CHARGE=80,
> STATEINF(81)%FIRST_STATE=5, STATEINF(81)%NUM_ATOMS=18,
> STATEINF(81)%NUM_STATES=3, STATEINF(82)%FIRST_ATOM=5671,
> STATEINF(82)%FIRST_CHARGE=134, STATEINF(82)%FIRST_STATE=8,
> STATEINF(82)%NUM_ATOMS=19, STATEINF(82)%NUM_STATES=5,
> STATEINF(83)%FIRST_ATOM=5751, STATEINF(83)%FIRST_CHARGE=0,
> STATEINF(83)%FIRST_STATE=0, STATEINF(83)%NUM_ATOMS=16,
> STATEINF(83)%NUM_STATES=5, STATEINF(84)%FIRST_ATOM=5840,
> STATEINF(84)%FIRST_CHARGE=0, STATEINF(84)%FIRST_STATE=0,
> STATEINF(84)%NUM_ATOMS=16, STATEINF(84)%NUM_STATES=5,
> STATEINF(85)%FIRST_ATOM=5929, STATEINF(85)%FIRST_CHARGE=273,
> STATEINF(85)%FIRST_STATE=15, STATEINF(85)%NUM_ATOMS=21,
> STATEINF(85)%NUM_STATES=2, STATEINF(86)%FIRST_ATOM=6022,
> STATEINF(86)%FIRST_CHARGE=134, STATEINF(86)%FIRST_STATE=8,
> STATEINF(86)%NUM_ATOMS=19, STATEINF(86)%NUM_STATES=5,
> STATENE=0.000000,38.759876,38.759876,38.759876,38.759876,
> 0.000000,-11.711591,
> -16.243597,0.000000,21.248624,21.248624,21.248624,21.
> 248624,-0.845507,0.000000,
> 0.000000,-78.199991,89.288609,0.000000,
> TRESCNT=87,CPHFIRST_SOL=6158, CPH_IGB=2, CPH_INTDIEL=1.0,
> /
>
> and here's the mdin file for production run step
>
> Explicit solvent constant pH MD
> &cntrl
> imin=0,irest=1,ntx=5,ntxo=2,
> ntpr=1000,ntwx=1000,nstlim=1000000,
> dt=0.002,ntt=3,tempi=300,
> temp0=300,gamma_ln=5.0,ig=-1,
> ntc=2,ntf=2,cut=8,iwrap=1,
> ioutfm=1,icnstph=2,ntcnstph=100,
> solvph=9.0,ntrelax=100,saltcon=0.1,
> /
>
> I've checked the cpin file but still can't figure out the problem.
> Can you help me?
>
> thank you.
>
> On Tue, Mar 7, 2017 at 8:25 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>> Hi
>>
>> The error message says that your cpin file has a bad variable defined,
>> "residue:"
>>
>> Can you check on that ?
>>
>> We need to see your cpin and mdin files before we can help you with this.
>>
>> adrian
>>
>>
>>
>> On 3/7/17 1:05 AM, EGIDEA PUTI DEVINA wrote:
>>> Hi,
>>> I'm trying to run explicit solvent cphmd based on tutorial from
>>> http://jswails.wikidot.com/explicit-solvent-constant-ph-md
>>> But I did some changes in file* tleap.in <http://tleap.in>* because my
>>> protein needs additional ion force field params.
>>>
>>> I also did changes for *cpinutil.py *because I want to titrate some base
>>> residues, so I added residues in -resnames.
>>> I used this following command for
>>> *cpinutil.py*
>>>
>>> cpinutil.py -p ppd2.solv10.parm7 -igb 2 -o ppd2.solv10.cpin -op
>>> ppd2.solv10.modO.parm7 -resnames AS4 GL4 HIP LYS TYR CYS
>>>
>>> and it successfully gave the ppd2.solv0.cpin and ppd2.solv0.modO.parm7.
>>>
>>> then I continued minimization, heating, and equilibration steps just
>>> like the tutorial.
>>>
>>> but when I ran the production step, appears an error like this:
>>>
>>> At line 164 of file constantph.F90 (unit = 23, file =
>> 'top/ppd2.solv10.cpin')
>>> Fortran runtime error: Cannot match namelist object name 'residue:
>>>
>>> Can you help me to solve this problems?
>>>
>>> Thankyou.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> --
>> Dr. Adrian E. Roitberg
>> University of Florida Research Foundation Professor.
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 08 2017 - 08:00:03 PST
