VMD-L Mailing List

From: ABEL Stephane (Stephane.ABEL_at_cea.fr)
Date: Tue Aug 07 2018 - 05:17:10 CDT

Hi James

>> Did you use VMD to write the PDB? Which plugin?
No, I modified manually the PDB file obtained from CHARMM-GUI and used it to obtain the *.gau. So you are right by eliminating the space, it worked.

>> Also, beware that fixed charge force fields don’t do a very good job for halogens; see for example
Thank you for the advice and the reference of the paper. I will read it.

Best

Stéphane

________________________________________
De : JC Gumbart [gumbart_at_physics.gatech.edu]
Envoyé : lundi 6 août 2018 18:34
À : ABEL Stephane
Cc : vmd-l_at_ks.uiuc.edu
Objet : Re: vmd-l: Derivation of parameters for a ligand with a Cl atom with fftk

Hi,

This seems to be a spacing problem in the PDB. VMD (and FFTK) read the element from columns 77 and 78 of the PDB file as given in the PDB spec, but in yours, it’s written in columns 78 and 79, and hence getting read as a carbon. Did you use VMD to write the PDB? Which plugin?

In the meantime, you can just eliminate one space, and it should be read correctly.

Also, beware that fixed charge force fields don’t do a very good job for halogens; see for example https://www.ncbi.nlm.nih.gov/pubmed/27353885 . We are thinking about ways to at least make it a little less bad by placing the water molecule in a couple different orientations as suggested here (although in the context of Drude): https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b01086

Best,
JC

On Aug 6, 2018, at 9:21 AM, ABEL Stephane <Stephane.ABEL_at_cea.fr<mailto:Stephane.ABEL_at_cea.fr>> wrote:

Dear all,

I would like to use fftk to derive parameters for the PK11195* (N-[(2R)-butan-2-yl]-1-(2-chlorophenyl)-N-methylisoquinoline-3-carboxamide) ligand and I have two questions:

1) Since this molecule contains a chlorine atom can I use the default procedure of fftk to derive the charge and the bonded parameters ?
2) When I use fftk (v.192) to obtain the Gaussian input file and specify in the last column of the PDB the atom chemical nature "Cl" (see below), in the Gaussian input file, the chlorine atom is changed to a carbon atom and consequently GAUSSIAN stops with the following error "The combination of multiplicity 1 and 175 electrons is impossible". How to modify the file gau and/or the PDB file to avoid this error ?

*https://www.sigmaaldrich.com/catalog/product/sigma/c0424?lang=fr&region=FR&gclid=Cj0KCQjw45_bBRD_ARIsAJ6wUXS2mO2hsricx1-Tu9MeYocW-jxiqFzIsK5lg4SOAdv7Dg_oayrKQtkaAgHIEALw_wcB

** ATOM 14 Cl1 PKA H 201 7.326 4.965 2.664 1.00 0.00 Cl

Thank you

Stéphane