[gmx-users] CgenFF conversion failed

[Justin Lemkul]

For those interested, the issue is in the NetworkX 2.0 package for 
Python. Version 1.11 produces correct output, but 2.0 fails. I suspect 
this is the root issue of all the recent complaints about the conversion 
script failing.

Thanks to Albert for helping debug this finally.

-Justin

On 11/19/17 1:40 PM, Albert wrote:
> file sent to you private email address.
>
> thx a lot
>
>
> On 11/19/2017 06:06 PM, Justin Lemkul wrote:
>>
>>
>> On 11/19/17 11:34 AM, Albert wrote:
>>> Hello,
>>>
>>> I generated a ligand.str file from Parachem website. Then, I try to 
>>> convert it to Gromacs format with command line:
>>>
>>> >cgenff_charmm2gmx.py UNK ligand.mol2 ligand.str charmm36-jul2017.ff
>>>
>>>
>>> However, the job always failed with the following messages:
>>>
>>> NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, 
>>> Jul 01 2016, 15:36:53) [GCC]
>>>
>>> NOTE2: Please be sure to use the same version of CGenFF in your 
>>> simulations that was used during parameter generation:
>>> --Version of CGenFF detected in  ligand.str : 4.0
>>> --Version of CGenFF detected in charmm36-jul2017.ff/forcefield.doc : 
>>> 4.0
>>>
>>> NOTE3: In order to avoid duplicated parameters, do NOT select the 
>>> 'Include parameters that are already in CGenFF' option when 
>>> uploading a molecule into CGenFF.
>>> Traceback (most recent call last):
>>>   File "/home/albert/bin/cgenff_charmm2gmx.py", line 799, in <module>
>>>     m.read_charmm_rtp(rtplines,atomtypes)
>>>   File "/home/albert/bin/cgenff_charmm2gmx.py", line 540, in 
>>> read_charmm_rtp
>>>     self.G.add_node(self.natoms, atm[self.natoms])
>>> TypeError: add_node() takes exactly 2 arguments (3 given)
>>>
>>>
>>> I didn't select the 'Include parameters that are already in CGenFF' 
>>> option when uploading a molecule into CGenFF.
>>>
>>
>> That's not relevant to this error.
>>
>>>
>>> Does anybody have any idea how to solve this problem?
>>>
>>
>> I have had this problem reported to me several times, yet I have 
>> never been able to reproduce it. I am beginning to suspect a bug in 
>> networkx or some weird versioning issue. If you send me your files 
>> (.str and .mol2) off-list, I will look at it, but unless I am able to 
>> reproduce the issue, there's not going to be anything I can do.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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