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UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1
#37813 02/03/20 11:47 AM
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santanu Offline OP
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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 CD2O1A OD2C1A LPDO1 (ATOMS 8 9 11)

Charm++ fatal error:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 (ATOMS 8 9 11)

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

Re: UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1
santanu #37814 02/03/20 02:25 PM
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This seems more like a NAMD question, please consult NAMD support.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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