From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Wed Dec 08 2021 - 18:26:27 CST
Dear Denilson,
Dummy bonds between lonepair 'atoms' and real atoms were dropped early in
development, so there shouldn't be a bond present - see a relatively recent
discussion here:
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/1020.html.
It's been a little while since I've dealt with this, but if I recall
correctly, older versions of NAMD don't handle these lone pairs
appropriately - try your simulation with the latest version of NAMD
available. If you're running this via HPC and it doesn't have NAMD 2.14,
you can test it locally to see if it gets past this error. Otherwise, you
might be able to try the 'lonepairs on' command mentioned in that mailing
list post I've linked to.
Hopefully that's helpful!
Regards,
Michael Robinson
On Thu, 9 Dec 2021 at 00:42, DENILSON FERREIRA DE OLIVEIRA <denilson_at_ufla.br>
wrote:
> 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!uwDckfP_YOefcgj9XsBWR63OEznQu2jSMAUBsZkqU5KjBxZJRMHjt0S-210JOGWeRg$
> <https://urldefense.com/v3/__https://cgenff.umaryland.edu/__;!!DZ3fjg!ocLi3tymD9reCRvyyWWIJnBKcbtuFXTWOkcD7neGAJZgYrT8GisQJisI3T7Vhik8LA$>
> )
>
> 2) In such str file I can find the following:
> ...
> ATOM LP1 LPH 0.050 ! lonepair on chlorine
> ...
> LONEPAIR COLI LP1 Cl1 C19 DIST 1.6400 SCAL 0.0 ! lonepair on
> chlorine
>
> 2) Using the topology files contained in toppar_c36_jul21.tgz, which is
> available through the MacKerell Lab Homepage (
> https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtml*charmm__;Iw!!DZ3fjg!uwDckfP_YOefcgj9XsBWR63OEznQu2jSMAUBsZkqU5KjBxZJRMHjt0S-212g7m9RmA$
> <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.
>
>
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