Hello Yao,
In explicit solvent, the prmtop file you point as an output in the flag -op in the cpinutil.py command is the one you need to use in the sander command. According to the commands you sent, it seems you are using a different file in your sander command.
Also, check your 01_min.in file to make sure you are not activating the constant pH option during the minimization run.
I hope this helps,
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633<tel:+1(352)846-1633>
On May 29, 2018, at 3:55 AM, 李耀 <liyao17.mails.tsinghua.edu.cn<mailto:liyao17.mails.tsinghua.edu.cn>> wrote:
My command to generate new topology file and cpin file is:
cpinutil.py -resnames GL4 AS4 -p prmtop \-op new_radii_prmtop -resnames HIP GL4 AS4 -igb 2 -o cpin
-----原始邮件-----
发件人:"李耀" <liyao17.mails.tsinghua.edu.cn<mailto:
liyao17.mails.tsinghua.edu.cn>>
发送时间:2018-05-29 10:35:06 (星期二)
收件人: amber <amber.ambermd.org<mailto:amber.ambermd.org>>
抄送:
主题: AMBER: trouble while running constant pH simulation
Hi all,
I'm trying to run constant pH simulation in explicit solvent model with Amber16(AmberTools17). I generated a cpin file according to the tutorial and type command:
sander -O -i 01_min.in -o 01_min.out -p radii_prmtop -c inpcrd -r 01_min.rst -inf 01_min.mdinfo -cpin cpin
to run minimization. It came out like this:
At line 174 of file constantph.F90 (unit = 18, file = 'cpin')
Fortran runtime error: Cannot match namelist object name 'residue:
And this is a part of my cpin file:
&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,
PROTCNT=2,1,1,0,1,1,1,1,0,1,1,1,1,
RESNAME='System: Unknown','Residue: HIP 33','Residue: AS4 38',
'Residue: GL4 39','Residue: GL4 57','Residue: AS4 67','Residue: HIP 70',
'Residue: GL4 73','Residue: GL4 83','Residue: AS4 86','Residue: AS4 91',
'Residue: GL4 92','Residue: GL4 96','Residue: AS4 100','Residue: GL4 116',
Is that a problem about my fortran compiler or about the file? I have no idea. Can you have a look on this? Many many thanks!
Yours sincerely,
Yao Li
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Received on Tue May 29 2018 - 06:00:02 PDT
