From: Santanu Santra (santop420_at_gmail.com)
Date: Sun Feb 02 2020 - 22:00:48 CST
Hi everyone,
I tried to model one model protein in drude forcefield
(toppar_drude_master_protein_2013f.str) and successfully generated the
structure by psfgen. But when I am trying to minimize it in namd, it is
showing some error throwing message of "unable to find the angle parameter
for lone pairs and two other atoms". I checked the ANGLE section in the
*.str file to find the combination of these three atoms but it was not
there.
Can anyone please suggest me where from I can get the Ktheta and
Theta0values for those angles including lone pair as one of these three
atoms.
Exact error log is ::::
=====================================================
*------------- Processor 0 Exiting: Called CmiAbort ------------Reason:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR LPD OD2C1A LPD (ATOMS 91
87 92)Charm++ fatal error:FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR
LPD OD2C1A LPD (ATOMS 91 87 92)Aborted (core dumped)*
*==================================================*
The section of pdb for which it is throwing error is as follows :
================================================
ATOM 8 C GLY 1 -2.504 6.616 3.758 1.00 0.00
XXX C
ATOM 9 O GLY 1 -1.357 7.045 3.786 1.00 0.00
XXX O
ATOM 10 LPOA GLY 1 -0.585 6.409 3.797 0.00 0.00
XXX H
ATOM 11 LPOB GLY 1 -1.192 8.031 3.797 0.00 0.00
XXX H
===========================================================
Any kind of suggestion is highly accepted.
Thanks and regards
Santanu Santra
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:12 CST