I want to do GROMACS simulation using ffamber_99sb forcefield. so that i have to generate the topology of the small molecules by ACPYPE. So can you tell me how to install ACPYPE and Anteamber installation together? Thanks in Advance.
Hello everyone,
Luckily i solved the problem like this:
Before installation of Ambertools, we have to install conda platform which allows you to install ambertools and other software packages. but it is compiled with python platform.
System requirements
32- or 64-bit computer. For Miniconda—400 MB disk space. For Anaconda—Minimum 3 GB disk space to download and install. Windows, macOS or Linux. Python 2.7, 3.4, 3.5 or 3.6.
1) Download Anaconda: from: https://conda.io/docs/user-guide/install/linux.html
2) In your Terminal window, run: bash Anaconda-latest-Linux-x86_64.sh Follow the prompts on the installer screens.
If you are unsure about any setting, accept the defaults. You can change them later.
To make the changes take effect, close and then re-open your Terminal window.
Now download the ambertools:
Binary Distribution via Conda: conda install ambertools=18 -c http://ambermd.org/download/ambertools/conda
ACPYPE installation: git clone https://github.com/alanwilter/acpype.git Enter in the acpype folder and type `ln -s $PWD/acpype.py /usr/local/bin/acpype` the ACPYPE program can now be used.
Thats it.
Dear Sourav,
I have followed the same steps whatever you have given above. But i can not run my Amber tool. I am installing the amber tools in the Windows 10 Ubuntu plugin. My installation path is AMBERHOME = /root/anaconda3 (which is default)
Can you tell me how can i set the path or this path will work for me.
If this path will work for me then What is the problem.
The error massage I am pasting below
is this related to path set problem or else? The charge of the ligand is 0.
=========================================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2020-07-25T09:06:13CEST (c) 2020 AWSdS |
=========================================================================================
WARNING: no 'babel' executable, no PDB file as input can be used!
WARNING: no charge value given, trying to guess one...
==> ... charge set to 0
==> Executing Antechamber...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Welcome to antechamber 19.0: molecular input file processor.
Info: Finished reading file (FFF.mol2); atoms read (63), bonds read (65).
Running: /root/anaconda3/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
---Judge bond type for Residue 1 with ID of 1 and Name of PHE ---
---Judge bond type for Residue 2 with ID of 2 and Name of PHE ---
---Judge bond type for Residue 3 with ID of 3 and Name of PHE ---
Running: /root/anaconda3/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 244; net charge: 0
Running: /root/anaconda3/bin/sqm -O -i sqm.in -o sqm.out
/root/anaconda3/bin/sqm: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
/root/anaconda3/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot properly run "/root/anaconda3/bin/sqm -O -i sqm.in -o sqm.out".
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Cannot open file (FFF_bcc_gaff.mol2) with mode (r).
No such file or directory
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'FFF_AC.prmtop'
Total time of execution: 1s
Arvind K Yadav I had a similar issue while trying to use acpype. It turns out the issue is in the version of python I was using is too recent (Python 3.8).
To change the version of python in conda, use the command:
conda install python=3.7.0
Then install acpype using:
conda install -c acpype acpype
Hope that helps.
Arvind K Yadav Sorry. I can't find out any solution. But I can make you assure that if you followed the steps on the LINUX platform, it will be alright.
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