Namd can not find parameters for chlorine lonepairs

From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_ufla.br)
Date: Wed Dec 08 2021 - 07:38:24 CST

Dear all,

1) The str file was generated for an organic substance containing a
chlorine atom, using the CHARMM General Force Field (CGenFF) program
version 2.5, through the Paramchem website (https://urldefense.com/v3/__https://cgenff.umaryland.edu/__;!!DZ3fjg!ocLi3tymD9reCRvyyWWIJnBKcbtuFXTWOkcD7neGAJZgYrT8GisQJisI3T7Vhik8LA$ )

2) In such str file I can find the following:
..
ATOM LP1 LPH 0.050 ! lonepair on chlorine
..
LONEPAIR COLI LP1 Cl1 C19 DIST 1.6400 SCAL 0.0 ! lonepair on
chlorine

2) Using the topology files contained in toppar_c36_jul21.tgz, which is
available through the MacKerell Lab Homepage (
https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtml*charmm__;Iw!!DZ3fjg!ocLi3tymD9reCRvyyWWIJnBKcbtuFXTWOkcD7neGAJZgYrT8GisQJisI3T7shi9Q0w$ ), as well as the str
file generated in Paramchem, I prepared the pdb and psf files using VMD
1.9.4a55. In the pdb file the lone pair of the chlorine atom is treated as
an atom:
...
ATOM 53428 LP1 UNK Z 1 226.355 227.015 173.583 1.00 0.00 ZO1
 X
...

3) In the configuration file to carry out calculations with Namd 2.14 I
have provided all the parameter files. The following is observed in the
output from Namd:

"...
Info: PARAMETERS ./par_all36m_prot.prm
Info: PARAMETERS ./par_all36_lipid.prm
Info: PARAMETERS ./par_all36_carb.prm
Info: PARAMETERS ./par_all36_na.prm
Info: PARAMETERS ./par_all36_cgenff.prm
Info: PARAMETERS ./toppar_all36_carb_glycopeptide.str
Info: PARAMETERS ./toppar_water_ions_namd.str
Info: PARAMETERS ./E2_ZINC000006181820_1-19_1-COR.str ! this is
the str file generated in Paramchem
"

4) However, Namd 2.14 did not perform the calculations because it
encountered an error:

"FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CLGR1 LPH (ATOMS 53428
53397)"

5) It means that Namd can not find parameters for the "bond" between the
chlorine atom and its lonepair of electrons.

I would appreciate it if somebody could be kind enough to help me to solve
this problem.

Best regards.

Denilson.

-- 
O conteúdo deste e-mail e anexos são restritos aos seus destinatários e de 
responsabilidade do remetente. O uso do e-mail deve estar de acordo com os 
regulamentos institucionais vigentes.

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST