Hi David,
Sorry to reply you late.
1. As I failed to use FEW, I calculated all I need manually by batch processing with MMPBSA.py.
However, I also got some trouble in using MMPBSA.py. It is very strange that some of my complexes cannot be calculated by the same procedures and program. I mean I have about 200 complexes. And now half of them successfully got the output .dat file from MMPBSA.py but the rest of them do not.
The error message is shown below:
Loading and checking parameter files for compatibility...
File "/home/zhonghua/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File "/home/zhonghua/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 610, in loadcheck_prmtops
self.normal_system.Map(INPUT['receptor_mask'], INPUT['ligand_mask'])
File "/home/zhonghua/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py", line 242, in Map
"this is not the case.")
PrmtopError: Couldn't predict mask from topology files!
Your ligand residues must be sequential in your complex.
There are likely problems with your topology files if this is not the case.
Exiting. All files have been retained.
2. As for the problem for using FEW,
A) If I use SDF file as the input of ligand structures, it will output a multiple-structure mol2 file. The error is:
#####################################################
# #
# FEW #
# Free Energy Workflow #
# #
#####################################################
Checking input parameters and files.
ERROR: Problem in Babel conversion of sdf-format to mol2-format. Please consult the file
/home/zhonghua/disk/FEW/babel.log for details.
~/babel.log:
195 molecules converted
2537 audit log messages
B) if I use multiple-structure mol2 file converted from SDF file by Babel as the input, part of the error is:
#####################################################
# #
# FEW #
# Free Energy Workflow #
# #
#####################################################
Checking input parameters and files.
WARNING:
The residue name in the ligand file /home/zhonghua/disk/FEW/structs/Lig_ligprep_434.maegz:1.mol2
you provided is longer than three characters and will be shortened
to the first three characters.
ERROR:
The atom names in the mol2-file /home/zhonghua/disk/FEW/structs/Lig_ligprep_434.maegz:1.mol2
are not unique. The atom name C is present at least twice.
Please ensure that the atom names in the ligand mol2-files are unique.
ERROR:
The atom names in the mol2-file /home/zhonghua/disk/FEW/structs/Lig_ligprep_434.maegz:1.mol2
are not unique. The atom name C is present at least twice.
Please ensure that the atom names in the ligand mol2-files are unique.
ERROR:
The atom names in the mol2-file /home/zhonghua/disk/FEW/structs/Lig_ligprep_434.maegz:1.mol2
are not unique. The atom name C is present at least twice.
Please ensure that the atom names in the ligand mol2-files are unique.
As shown as all above, the residue name (more than 3 characters) and the atom name (without serial numbers) cannot be recognised by FEW. The programs I use are Maestro and Babel as required in Amber manual. So I am looking for a program which can generate the input structures well recognised by FEW.
Thank you very much and kind regards,
Zhonghua
> On 17. Apr 2019, at 14:06, David A Case <david.case.rutgers.edu> wrote:
>
> On Wed, Apr 17, 2019, Zhonghua Xia wrote:
>>
>> I want to use FEW to expediently batch processing ligands. But I got into
>> trouble at the very beginning (using the command file leap_am1). The
>> problem is no matter which tool I use to convert my ligands’ file to mol2
>> format, FEW just can’t recognise it. Even though I use sdf files, it
>> can’t recognise it either. The tools I tried are Maestro, Babel and VMD.
>
> It would be great if you could post one of the mol2 files that failed,
> plus the exact error message.
>
> ...thanks...dac
>
>
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Received on Tue Apr 30 2019 - 08:00:02 PDT
