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

From: Nirmitee Mulgaonkar (nirmitee.mulgaonkar_at_tamu.edu)
Date: Wed Jul 10 2019 - 01:02:53 CDT

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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