[AMBER] How to run npt simulation if IFBOX=0 in .prmtop file?

From: Dongshan Wei <dswei0523.gmail.com>
Date: Thu, 10 Oct 2013 20:43:30 +0800

Hi all,

I met one problem when I try to run npt simulation for my melamine
supercell system. The error is as follows:

"(NTB /= 0 && NTP /= 0) but IFBOX == 0

 This combination is not supported"

I checked the .prmtop file corresponding to the melamine supercell and
found the IFBOX value is exactly 0. So my question is how to change the
setting in .prmtop to let run NPT simulation for the supercell system?

I created the melamine supercell in the following precedure:
(1) create a pdb file for a melamine molecule and used the GAFF force filed
and the R.E.D. charge fitting tool to obtain the .prmtop and .inpcrd files
for the single melamine molecule.
(2) Use the propPDB command to create a 4x4x8 melamine supercell and the
corresponding pdb file. Through the supercell's pdb, create the melamine
supercell's .prmtop and .inpcrd files.
(3) execute a minimization for the obtained supercell in vacuum.
(4) Using the minimized .mdcrd file and the supercell's .prmtop to run a
short NVT simulation. In this step I updated the .mdcrd file and added a
line of "200.0 200.0 200.0 90.0 90.0 90.0" in the bottom of the .mdcrd
file to contain the supercell into a box and use periodic boundary
conditions in NVT simulation.

After the short-time NVT simulation, I begun to perform NPT simulation with
the supercell's .prmtop and the obtained .mdcrd in NVT, I met the above
problem. So could you please tell me what problems exist in my simulation
protocol´╝čThe melamine supercell's prmtop and coordinate files for NPT
simulation are attached.

Thanks a lot in advance!


Dongshan Wei, Dr.
Chongqing Institute of Green and Intelligent Technology, CAS
85 Jinyu Ave, Yubei Area, Chongqing 401120, China
Email: dswei.cigit.ac.cn <dswei.cigit.cas.cn>
Phone: (+86) 23-65935641

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Received on Thu Oct 10 2013 - 06:00:04 PDT
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