Greetings Amber users:
I was wondering if you be kind to help a biochemist in disgrace :)
I have this output:
$ sander -O -i input.in -c prmcrd -o output.out -cpin cpin
-cpout cpout -cprestrt cprestrt -r rstPGFIO-F-233/namelist
read/unit=18/too many constants to initialize group item.
File name = cpin formatted, sequential access record = 29
In source file _mdread.f, at line number 1308
$
My cpin file looks fine, any idea what is REALLY the output about?
please help!.
and here is my cpin file (could not upload it):
&CNSTPH
CHRGDAT=-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,-0.498,0.132,-0.103,0.132,0.5973,-0.5679,
-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,
-0.5727,0,0.1292,0.1147,0.7341,-0.5894,-0.3479,0.2747,-0.1354,0.1212,-0.1012,
0.0367,0.0367,0.1868,-0.5432,0,0.1635,0.1435,-0.2795,0.3339,-0.2207,0.1862,
0.7341,-0.5894,-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,
0.38604,0.38604,0.7341,-0.5894,
PROTCNT=1,0,2,1,1,3,2,
RESNAME='System: Unknown','Residue: TYR 15','Residue: HIP 21',
'Residue: TYR 25','Residue: TYR 29','Residue: TYR 33','Residue: TYR 44',
'Residue: LYS 68','Residue: LYS 70','Residue: TYR 71','Residue: LYS 87',
'Residue: LYS 89','Residue: LYS 91','Residue: LYS 95','Residue: HIP 104',
'Residue: LYS 106','Residue: LYS 116','Residue: HIP 146','Residue: LYS
149',
'Residue: LYS 164','Residue: LYS 174','Residue: LYS 181','Residue: TYR
207',
'Residue: LYS 212','Residue: LYS 213','Residue: TYR 221','Residue: LYS
226',
'Residue: HIP 232','Residue: LYS 240','Residue: LYS 254','Residue: LYS
262',
'Residue: HIP 271','Residue: TYR 286','Residue: LYS 288','Residue: LYS
291',
'Residue: LYS 294','Residue: TYR 301','Residue: LYS 328','Residue: TYR
336',
'Residue: TYR 339','Residue: HIP 340','Residue: LYS 346','Residue: LYS
350',
'Residue: HIP 353','Residue: LYS 356','Residue: TYR 381','Residue: HIP
382',
'Residue: LYS 390','Residue: HIP 417','Residue: TYR 421','Residue: LYS
427',
'Residue: TYR 437','Residue: LYS 448','Residue: LYS 453','Residue: LYS
492',
'Residue: TYR 500','Residue: LYS 509','Residue: LYS 515','Residue: LYS
523',
'Residue: TYR 524','Residue: LYS 539',
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,STATEINF(0)%FIRST_ATOM=218,
STATEINF(0)%FIRST_CHARGE=0, STATEINF(0)%FIRST_STATE=0,
STATEINF(0)%NUM_ATOMS=21, STATEINF(0)%NUM_STATES=2,
STATEINF(1)%FIRST_ATOM=304, STATEINF(1)%FIRST_CHARGE=42,
STATEINF(1)%FIRST_STATE=2, STATEINF(1)%NUM_ATOMS=18,
STATEINF(1)%NUM_STATES=3,
STATEINF(2)%FIRST_ATOM=369, STATEINF(2)%FIRST_CHARGE=0,
STATEINF(2)%FIRST_STATE=0, STATEINF(2)%NUM_ATOMS=21,
STATEINF(2)%NUM_STATES=2,
STATEINF(3)%FIRST_ATOM=429, STATEINF(3)%FIRST_CHARGE=0,
STATEINF(3)%FIRST_STATE=0, STATEINF(3)%NUM_ATOMS=21,
STATEINF(3)%NUM_STATES=2,
STATEINF(4)%FIRST_ATOM=500, STATEINF(4)%FIRST_CHARGE=0,
STATEINF(4)%FIRST_STATE=0, STATEINF(4)%NUM_ATOMS=21,
STATEINF(4)%NUM_STATES=2,
STATEINF(5)%FIRST_ATOM=664, STATEINF(5)%FIRST_CHARGE=0,
STATEINF(5)%FIRST_STATE=0, STATEINF(5)%NUM_ATOMS=21,
STATEINF(5)%NUM_STATES=2,
STATEINF(6)%FIRST_ATOM=1014, STATEINF(6)%FIRST_CHARGE=96,
STATEINF(6)%FIRST_STATE=5, STATEINF(6)%NUM_ATOMS=22,
STATEINF(6)%NUM_STATES=2,
STATEINF(7)%FIRST_ATOM=1048, STATEINF(7)%FIRST_CHARGE=96,
STATEINF(7)%FIRST_STATE=5, STATEINF(7)%NUM_ATOMS=22,
STATEINF(7)%NUM_STATES=2,
STATEINF(8)%FIRST_ATOM=1070, STATEINF(8)%FIRST_CHARGE=0,
STATEINF(8)%FIRST_STATE=0, STATEINF(8)%NUM_ATOMS=21,
STATEINF(8)%NUM_STATES=2,
STATEINF(9)%FIRST_ATOM=1342, STATEINF(9)%FIRST_CHARGE=96,
STATEINF(9)%FIRST_STATE=5, STATEINF(9)%NUM_ATOMS=22,
STATEINF(9)%NUM_STATES=2,
STATEINF(10)%FIRST_ATOM=1371, STATEINF(10)%FIRST_CHARGE=96,
STATEINF(10)%FIRST_STATE=5, STATEINF(10)%NUM_ATOMS=22,
STATEINF(10)%NUM_STATES=2, STATEINF(11)%FIRST_ATOM=1400,
STATEINF(11)%FIRST_CHARGE=96, STATEINF(11)%FIRST_STATE=5,
STATEINF(11)%NUM_ATOMS=22, STATEINF(11)%NUM_STATES=2,
STATEINF(12)%FIRST_ATOM=1462, STATEINF(12)%FIRST_CHARGE=96,
STATEINF(12)%FIRST_STATE=5, STATEINF(12)%NUM_ATOMS=22,
STATEINF(12)%NUM_STATES=2, STATEINF(13)%FIRST_ATOM=1612,
STATEINF(13)%FIRST_CHARGE=42, STATEINF(13)%FIRST_STATE=2,
STATEINF(13)%NUM_ATOMS=18, STATEINF(13)%NUM_STATES=3,
STATEINF(14)%FIRST_ATOM=1649, STATEINF(14)%FIRST_CHARGE=96,
STATEINF(14)%FIRST_STATE=5, STATEINF(14)%NUM_ATOMS=22,
STATEINF(14)%NUM_STATES=2, STATEINF(15)%FIRST_ATOM=1805,
STATEINF(15)%FIRST_CHARGE=96, STATEINF(15)%FIRST_STATE=5,
STATEINF(15)%NUM_ATOMS=22, STATEINF(15)%NUM_STATES=2,
STATEINF(16)%FIRST_ATOM=2285, STATEINF(16)%FIRST_CHARGE=42,
STATEINF(16)%FIRST_STATE=2, STATEINF(16)%NUM_ATOMS=18,
STATEINF(16)%NUM_STATES=3, STATEINF(17)%FIRST_ATOM=2339,
STATEINF(17)%FIRST_CHARGE=96, STATEINF(17)%FIRST_STATE=5,
STATEINF(17)%NUM_ATOMS=22, STATEINF(17)%NUM_STATES=2,
STATEINF(18)%FIRST_ATOM=2578, STATEINF(18)%FIRST_CHARGE=96,
STATEINF(18)%FIRST_STATE=5, STATEINF(18)%NUM_ATOMS=22,
STATEINF(18)%NUM_STATES=2, STATEINF(19)%FIRST_ATOM=2729,
STATEINF(19)%FIRST_CHARGE=96, STATEINF(19)%FIRST_STATE=5,
STATEINF(19)%NUM_ATOMS=22, STATEINF(19)%NUM_STATES=2,
STATEINF(20)%FIRST_ATOM=2845, STATEINF(20)%FIRST_CHARGE=96,
STATEINF(20)%FIRST_STATE=5, STATEINF(20)%NUM_ATOMS=22,
STATEINF(20)%NUM_STATES=2, STATEINF(21)%FIRST_ATOM=3255,
STATEINF(21)%FIRST_CHARGE=0, STATEINF(21)%FIRST_STATE=0,
STATEINF(21)%NUM_ATOMS=21, STATEINF(21)%NUM_STATES=2,
STATEINF(22)%FIRST_ATOM=3322, STATEINF(22)%FIRST_CHARGE=96,
STATEINF(22)%FIRST_STATE=5, STATEINF(22)%NUM_ATOMS=22,
STATEINF(22)%NUM_STATES=2, STATEINF(23)%FIRST_ATOM=3344,
STATEINF(23)%FIRST_CHARGE=96, STATEINF(23)%FIRST_STATE=5,
STATEINF(23)%NUM_ATOMS=22, STATEINF(23)%NUM_STATES=2,
STATEINF(24)%FIRST_ATOM=3469, STATEINF(24)%FIRST_CHARGE=0,
STATEINF(24)%FIRST_STATE=0, STATEINF(24)%NUM_ATOMS=21,
STATEINF(24)%NUM_STATES=2, STATEINF(25)%FIRST_ATOM=3561,
STATEINF(25)%FIRST_CHARGE=96, STATEINF(25)%FIRST_STATE=5,
STATEINF(25)%NUM_ATOMS=22, STATEINF(25)%NUM_STATES=2,
STATEINF(26)%FIRST_ATOM=3647, STATEINF(26)%FIRST_CHARGE=42,
STATEINF(26)%FIRST_STATE=2, STATEINF(26)%NUM_ATOMS=18,
STATEINF(26)%NUM_STATES=3, STATEINF(27)%FIRST_ATOM=3749,
STATEINF(27)%FIRST_CHARGE=96, STATEINF(27)%FIRST_STATE=5,
STATEINF(27)%NUM_ATOMS=22, STATEINF(27)%NUM_STATES=2,
STATEINF(28)%FIRST_ATOM=3937, STATEINF(28)%FIRST_CHARGE=96,
STATEINF(28)%FIRST_STATE=5, STATEINF(28)%NUM_ATOMS=22,
STATEINF(28)%NUM_STATES=2, STATEINF(29)%FIRST_ATOM=4057,
STATEINF(29)%FIRST_CHARGE=96, STATEINF(29)%FIRST_STATE=5,
STATEINF(29)%NUM_ATOMS=22, STATEINF(29)%NUM_STATES=2,
STATEINF(30)%FIRST_ATOM=4211, STATEINF(30)%FIRST_CHARGE=42,
STATEINF(30)%FIRST_STATE=2, STATEINF(30)%NUM_ATOMS=18,
STATEINF(30)%NUM_STATES=3, STATEINF(31)%FIRST_ATOM=4413,
STATEINF(31)%FIRST_CHARGE=0, STATEINF(31)%FIRST_STATE=0,
STATEINF(31)%NUM_ATOMS=21, STATEINF(31)%NUM_STATES=2,
STATEINF(32)%FIRST_ATOM=4444, STATEINF(32)%FIRST_CHARGE=96,
STATEINF(32)%FIRST_STATE=5, STATEINF(32)%NUM_ATOMS=22,
STATEINF(32)%NUM_STATES=2, STATEINF(33)%FIRST_ATOM=4499,
STATEINF(33)%FIRST_CHARGE=96, STATEINF(33)%FIRST_STATE=5,
STATEINF(33)%NUM_ATOMS=22, STATEINF(33)%NUM_STATES=2,
STATEINF(34)%FIRST_ATOM=4551, STATEINF(34)%FIRST_CHARGE=96,
STATEINF(34)%FIRST_STATE=5, STATEINF(34)%NUM_ATOMS=22,
STATEINF(34)%NUM_STATES=2, STATEINF(35)%FIRST_ATOM=4661,
STATEINF(35)%FIRST_CHARGE=0, STATEINF(35)%FIRST_STATE=0,
STATEINF(35)%NUM_ATOMS=21, STATEINF(35)%NUM_STATES=2,
STATEINF(36)%FIRST_ATOM=5073, STATEINF(36)%FIRST_CHARGE=96,
STATEINF(36)%FIRST_STATE=5, STATEINF(36)%NUM_ATOMS=22,
STATEINF(36)%NUM_STATES=2, STATEINF(37)%FIRST_ATOM=5203,
STATEINF(37)%FIRST_CHARGE=0, STATEINF(37)%FIRST_STATE=0,
STATEINF(37)%NUM_ATOMS=21, STATEINF(37)%NUM_STATES=2,
STATEINF(38)%FIRST_ATOM=5257, STATEINF(38)%FIRST_CHARGE=0,
STATEINF(38)%FIRST_STATE=0, STATEINF(38)%NUM_ATOMS=21,
STATEINF(38)%NUM_STATES=2, STATEINF(39)%FIRST_ATOM=5278,
STATEINF(39)%FIRST_CHARGE=42, STATEINF(39)%FIRST_STATE=2,
STATEINF(39)%NUM_ATOMS=18, STATEINF(39)%NUM_STATES=3,
STATEINF(40)%FIRST_ATOM=5376, STATEINF(40)%FIRST_CHARGE=96,
STATEINF(40)%FIRST_STATE=5, STATEINF(40)%NUM_ATOMS=22,
STATEINF(40)%NUM_STATES=2, STATEINF(41)%FIRST_ATOM=5439,
STATEINF(41)%FIRST_CHARGE=96, STATEINF(41)%FIRST_STATE=5,
STATEINF(41)%NUM_ATOMS=22, STATEINF(41)%NUM_STATES=2,
STATEINF(42)%FIRST_ATOM=5478, STATEINF(42)%FIRST_CHARGE=42,
STATEINF(42)%FIRST_STATE=2, STATEINF(42)%NUM_ATOMS=18,
STATEINF(42)%NUM_STATES=3, STATEINF(43)%FIRST_ATOM=5520,
STATEINF(43)%FIRST_CHARGE=96, STATEINF(43)%FIRST_STATE=5,
STATEINF(43)%NUM_ATOMS=22, STATEINF(43)%NUM_STATES=2,
STATEINF(44)%FIRST_ATOM=5906, STATEINF(44)%FIRST_CHARGE=0,
STATEINF(44)%FIRST_STATE=0, STATEINF(44)%NUM_ATOMS=21,
STATEINF(44)%NUM_STATES=2, STATEINF(45)%FIRST_ATOM=5927,
STATEINF(45)%FIRST_CHARGE=42, STATEINF(45)%FIRST_STATE=2,
STATEINF(45)%NUM_ATOMS=18, STATEINF(45)%NUM_STATES=3,
STATEINF(46)%FIRST_ATOM=6046, STATEINF(46)%FIRST_CHARGE=96,
STATEINF(46)%FIRST_STATE=5, STATEINF(46)%NUM_ATOMS=22,
STATEINF(46)%NUM_STATES=2, STATEINF(47)%FIRST_ATOM=6436,
STATEINF(47)%FIRST_CHARGE=42, STATEINF(47)%FIRST_STATE=2,
STATEINF(47)%NUM_ATOMS=18, STATEINF(47)%NUM_STATES=3,
STATEINF(48)%FIRST_ATOM=6499, STATEINF(48)%FIRST_CHARGE=0,
STATEINF(48)%FIRST_STATE=0, STATEINF(48)%NUM_ATOMS=21,
STATEINF(48)%NUM_STATES=2, STATEINF(49)%FIRST_ATOM=6596,
STATEINF(49)%FIRST_CHARGE=96, STATEINF(49)%FIRST_STATE=5,
STATEINF(49)%NUM_ATOMS=22, STATEINF(49)%NUM_STATES=2,
STATEINF(50)%FIRST_ATOM=6740, STATEINF(50)%FIRST_CHARGE=0,
STATEINF(50)%FIRST_STATE=0, STATEINF(50)%NUM_ATOMS=21,
STATEINF(50)%NUM_STATES=2, STATEINF(51)%FIRST_ATOM=6897,
STATEINF(51)%FIRST_CHARGE=96, STATEINF(51)%FIRST_STATE=5,
STATEINF(51)%NUM_ATOMS=22, STATEINF(51)%NUM_STATES=2,
STATEINF(52)%FIRST_ATOM=6992, STATEINF(52)%FIRST_CHARGE=96,
STATEINF(52)%FIRST_STATE=5, STATEINF(52)%NUM_ATOMS=22,
STATEINF(52)%NUM_STATES=2, STATEINF(53)%FIRST_ATOM=7579,
STATEINF(53)%FIRST_CHARGE=96, STATEINF(53)%FIRST_STATE=5,
STATEINF(53)%NUM_ATOMS=22, STATEINF(53)%NUM_STATES=2,
STATEINF(54)%FIRST_ATOM=7717, STATEINF(54)%FIRST_CHARGE=0,
STATEINF(54)%FIRST_STATE=0, STATEINF(54)%NUM_ATOMS=21,
STATEINF(54)%NUM_STATES=2, STATEINF(55)%FIRST_ATOM=7861,
STATEINF(55)%FIRST_CHARGE=96, STATEINF(55)%FIRST_STATE=5,
STATEINF(55)%NUM_ATOMS=22, STATEINF(55)%NUM_STATES=2,
STATEINF(56)%FIRST_ATOM=7951, STATEINF(56)%FIRST_CHARGE=96,
STATEINF(56)%FIRST_STATE=5, STATEINF(56)%NUM_ATOMS=22,
STATEINF(56)%NUM_STATES=2, STATEINF(57)%FIRST_ATOM=8089,
STATEINF(57)%FIRST_CHARGE=96, STATEINF(57)%FIRST_STATE=5,
STATEINF(57)%NUM_ATOMS=22, STATEINF(57)%NUM_STATES=2,
STATEINF(58)%FIRST_ATOM=8111, STATEINF(58)%FIRST_CHARGE=0,
STATEINF(58)%FIRST_STATE=0, STATEINF(58)%NUM_ATOMS=21,
STATEINF(58)%NUM_STATES=2, STATEINF(59)%FIRST_ATOM=8299,
STATEINF(59)%FIRST_CHARGE=96, STATEINF(59)%FIRST_STATE=5,
STATEINF(59)%NUM_ATOMS=22, STATEINF(59)%NUM_STATES=2,
STATENE=0,-78.34438,0,-11.7817,-16.27078,-0.839279999999999,0,TRESCNT=60,
/
Eddie Men wrote:
> Greetings Amber users
>
> I am getting this message, when running amber:
>
> PGFIO-F-233/namelist read/unit=18/too many constants to initialize
> group item.
> File name = cpin formatted, sequential access record = 29
> In source file _mdread.f, at line number 1308
>
> My file was generated with cpinutil and it looks just fine, so I do
> not think the file itself is a problem,
> any ideas to what is going wrong?.
> I tried uploading the files here without success,
>
>
> eddie
>
>> cpin files are generally made by the "cpinutil.pl" file (see p. 173
>> of the
>> Users' Manual.) There is an example of running constant pH (including
>> a cpin file) in $AMBERHOME/test/cnstph.
>>
>> ....dac
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>>
>
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Received on Sun Oct 07 2007 - 06:07:34 PDT
