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.
On Tue, Jul 9, 2019 at 10:00 PM Aravinda Munasinghe <aravinda1879_at_gmail.com>
> 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.
> On Tue, Jul 9, 2019 at 9:25 PM Nirmitee Mulgaonkar <
> nirmitee.mulgaonkar_at_tamu.edu> wrote:
>> 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
>> I am using the following parameter files:
>> 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.
>> *Nirmitee Sanjay Mulgaonkar | Graduate Research Assistant*
>> Biological and Agricultural Engineering
>> Texas A&M University
> Aravinda Munasinghe,
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