Re: [AMBER] AMBER: trouble while running constant pH simulation

From: Cruzeiro,Vinicius Wilian D <>
Date: Tue, 29 May 2018 12:58:06 +0000

Hello Yao,

In explicit solvent, the prmtop file you point as an output in the flag -op in the 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 file to make sure you are not activating the constant pH option during the minimization run.

I hope this helps,

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 <<>> wrote:

My command to generate new topology file and cpin file is: -resnames GL4 AS4 -p prmtop \-op new_radii_prmtop -resnames HIP GL4 AS4 -igb 2 -o cpin

发件人:"李耀" <<>>
发送时间:2018-05-29 10:35:06 (星期二)
收件人: amber <<>>
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 -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:
                                            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
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