[gmx-users] CgenFF conversion failed

[Albert]

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.