VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Nov 18 2021 - 08:03:40 CST

Have you looked at the bonds in your psf to make sure they are correct?
This looks like you've hydrogen atoms that have two bonds...
Best,
Peter

On Thu, Nov 18, 2021 at 5:42 AM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> It seems thatb the str used is inadequate. Alsdo adjusting angles in str,
> namd assks for dihedrals
> fp
>
> On Thu, Nov 18, 2021 at 9:29 AM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> While attempting to minimize a CHCL3 box built from CHARMM36-provided
>> toppar_chloroform_dh.str, namd crashes
>>
>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5
>>> 4)
>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5
>>> 4)
>>>
>>
>> Actually, the prm part of the str (which was read by namd) l correctly
>> furnishes
>>
>>> ANGLES
>>> CLCM CCM CLCM 0.0 111.30
>>> HCM CCM CLCM 0.0 107.57
>>>
>>
>> Why is namd looking for those wrong angles? The central atom is carbon
>> not hydrogen.
>>
>> Thanks for advice
>> francesco pietra
>>
>