Dear Manju,
Are you sure you are using pmemd or sander from Amber18? The cpin format has changed from Amber16 to Amber18. pmemd and sander from Amber18 are able to process both cpin formats, however, pmemd and sander from Amber16 cannot process the newer format. If you have AmberTools18 but want to run Amber16, you should run cpinutil.py with the flag --old-format (manually removing the PKA_CORR line is going to yield wrong results!!!).
Best,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Manju Sah <manjusah.gmail.com>
Sent: Friday, December 21, 2018 6:45:32 AM
To: AMBER Mailing List
Subject: [AMBER] cpin file format issue in production run
Dear Amber Users,
I am doing explicit Constant pH simulation of peptide using amber18
version. I am getting following error in production run step.
*At line 164 of file constantph.F90 (unit = 23, file = 'test-hip.cpin')*
*Fortran runtime error: Bad data for namelist object statene*
Earlier i used amber16 for the similar type of calculation and didn't find
any error in production run.
Then I compared the cpin files generated by both the amber version and
found that the last 2nd and 3rd lines are different in both the files. Now
i am not sure which one is correct as STATENE in different. When I removed
below line from cpin file generated by amber18 , the production run is
going fine.
*PKA_CORR=7.1000,0.6000,0.0000,*
I wanted to know where is the problem ? Is there any information/reference
available about the file format of cpin/keyword used.
The output is as follows
*amber18*
&CNSTPH
CHRGDAT=-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,
PROTCNT=2,1,1,
RESNAME='System: Unknown','Residue: HIP 39','Residue: HIP 47',
'Residue: HIP 55','Residue: HIP 63','Residue: HIP 74','Residue: HIP 89',
RESSTATE=0,0,0,0,0,0,
STATEINF(0)%FIRST_ATOM=535, STATEINF(0)%FIRST_CHARGE=0,
STATEINF(0)%FIRST_STATE=0, STATEINF(0)%NUM_ATOMS=18,
STATEINF(0)%NUM_STATES=3,
STATEINF(1)%FIRST_ATOM=636, STATEINF(1)%FIRST_CHARGE=0,
STATEINF(1)%FIRST_STATE=0, STATEINF(1)%NUM_ATOMS=18,
STATEINF(1)%NUM_STATES=3,
STATEINF(2)%FIRST_ATOM=737, STATEINF(2)%FIRST_CHARGE=0,
STATEINF(2)%FIRST_STATE=0, STATEINF(2)%NUM_ATOMS=18,
STATEINF(2)%NUM_STATES=3,
STATEINF(3)%FIRST_ATOM=838, STATEINF(3)%FIRST_CHARGE=0,
STATEINF(3)%FIRST_STATE=0, STATEINF(3)%NUM_ATOMS=18,
STATEINF(3)%NUM_STATES=3,
STATEINF(4)%FIRST_ATOM=960, STATEINF(4)%FIRST_CHARGE=0,
STATEINF(4)%FIRST_STATE=0, STATEINF(4)%NUM_ATOMS=18,
STATEINF(4)%NUM_STATES=3,
STATEINF(5)%FIRST_ATOM=1216, STATEINF(5)%FIRST_CHARGE=0,
STATEINF(5)%FIRST_STATE=0, STATEINF(5)%NUM_ATOMS=18,
STATEINF(5)%NUM_STATES=3,
STATENE=0.000000,-2.776410,-6.483630,
PKA_CORR=7.1000,0.6000,0.0000,
TRESCNT=6,CPHFIRST_SOL=1372, CPH_IGB=2, CPH_INTDIEL=1.0,
/
*and the output from amber16 is *
&CNSTPH
CHRGDAT=-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,
PROTCNT=2,1,1,
RESNAME='System: Unknown','Residue: HIP 39','Residue: HIP 47',
'Residue: HIP 55','Residue: HIP 63','Residue: HIP 74','Residue: HIP 89',
RESSTATE=0,0,0,0,0,0,
STATEINF(0)%FIRST_ATOM=535, STATEINF(0)%FIRST_CHARGE=0,
STATEINF(0)%FIRST_STATE=0, STATEINF(0)%NUM_ATOMS=18,
STATEINF(0)%NUM_STATES=3,
STATEINF(1)%FIRST_ATOM=636, STATEINF(1)%FIRST_CHARGE=0,
STATEINF(1)%FIRST_STATE=0, STATEINF(1)%NUM_ATOMS=18,
STATEINF(1)%NUM_STATES=3,
STATEINF(2)%FIRST_ATOM=737, STATEINF(2)%FIRST_CHARGE=0,
STATEINF(2)%FIRST_STATE=0, STATEINF(2)%NUM_ATOMS=18,
STATEINF(2)%NUM_STATES=3,
STATEINF(3)%FIRST_ATOM=838, STATEINF(3)%FIRST_CHARGE=0,
STATEINF(3)%FIRST_STATE=0, STATEINF(3)%NUM_ATOMS=18,
STATEINF(3)%NUM_STATES=3,
STATEINF(4)%FIRST_ATOM=960, STATEINF(4)%FIRST_CHARGE=0,
STATEINF(4)%FIRST_STATE=0, STATEINF(4)%NUM_ATOMS=18,
STATEINF(4)%NUM_STATES=3,
STATEINF(5)%FIRST_ATOM=1216, STATEINF(5)%FIRST_CHARGE=0,
STATEINF(5)%FIRST_STATE=0, STATEINF(5)%NUM_ATOMS=18,
STATEINF(5)%NUM_STATES=3,
STATENE=0,-11.7115914534,-16.2435974337,
TRESCNT=6,CPHFIRST_SOL=1372, CPH_IGB=2, CPH_INTDIEL=1.0,
/
Thanks a lot.....
Manju Kumari
N-PDF
IIT Madras, India
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Received on Fri Dec 21 2018 - 07:00:01 PST
