Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220 1222)

From: Aravinda Munasinghe (aravinda1879_at_gmail.com)
Date: Wed Jul 10 2019 - 06:57:20 CDT

Yes. This is again about missing parameters. I would recomend you to go
over the topology. Looking at missing parameters, it is weird how you have
a C-H-C-H dihedral definition. Why dont you try getting the topology from
charmm cgenff website. And make sure the bond order is exactly what you
want.
https://cgenff.umaryland.edu/

On Wed, Jul 10, 2019, 2:02 AM Nirmitee Mulgaonkar <
nirmitee.mulgaonkar_at_tamu.edu> wrote:

> Thank you Aravinda. I did add the str file as you suggested. However, I
> received another error message:
>
> *FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG331 HGA3 CG2O1 HGA3
> (ATOMS 1216 1235 1217 1236)*
>
> I suppose this is another parameter analog which is not present in the str
> file as well. I did use swissparam to generate parameters; and the rtf &
> par files do have information regarding the analog but in a different
> format. I'm not sure if it is advisable to combine the two parameter files
> generated by cgenff and swissparam.
>
> Please suggest.
>
> Thanks,
> Nirmitee
>
>
>
> On Tue, Jul 9, 2019 at 10:00 PM Aravinda Munasinghe <
> aravinda1879_at_gmail.com> wrote:
>
>> You need to add the str file along with par_all36_cgenff.prm
>> par_all36_prot.prm to your configuration file. Since CHARMM using analog
>> parameters, not all are defined in distributed cgenff.
>> Best,
>> Aravinda
>>
>> On Tue, Jul 9, 2019 at 9:25 PM Nirmitee Mulgaonkar <
>> nirmitee.mulgaonkar_at_tamu.edu> wrote:
>>
>>> Hi,
>>>
>>> I am trying to run the minimization step for my simulation in NAMD.
>>>
>>> The log file showed the following error message:
>>> FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220
>>> 1222)
>>>
>>> I am using the following parameter files:
>>> par_all36_cgenff.prm
>>> par_all36_prot.prm
>>>
>>> I generated the str file for my ligand from
>>> https://cgenff.paramchem.org/
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__cgenff.paramchem.org_&d=DwMFaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=HIRwB_4N1DCrbGOu3hCs3LBKdu7aeEh4DQPMe_9_f1g&m=sSnYrLP8mAyNOzbC2bofa09i1StHYfpDQy1-MjAQhs8&s=2XLZzMmZ7iDHGF01_sxRWF7x5NeWGrn8mQ6udysS-1s&e=> using
>>> the mol2 file from ZINC15.
>>>
>>> I cannot find BOND PARAMETERS FOR CG2O4 CG311 in any of the parameter
>>> files from the recently updated toppar_c36_jul18.tgz
>>>
>>> Please let me know what can be done.
>>>
>>> Thanks,
>>> Nirmitee
>>>
>>> *Nirmitee Sanjay Mulgaonkar | Graduate Research Assistant*
>>> Biological and Agricultural Engineering
>>> Texas A&M University
>>>
>>
>>
>> --
>> Aravinda Munasinghe,
>>
>>

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