[gmx-users] Chlorine in PDBs

az adam.zalewski at mail.com
Fri Jul 24 14:36:54 CEST 2015

That's what I needed to hear! According to the topology the atom is 
perfectly fine.

Thanks a lot,

On 24-Jul-15 14:09, Smith, Micholas D. wrote:
> Adam,
> The topology file is the definitive atom-definiations used in the simulation. You just need to confirm that the Chlorine in your *.top has an matches the atomtype from  Amber99SB. As far as being written as C instead CL in the pdb, you could likely just use sed to find and replace these into CL so VMD treats them properly (a similar problem happens if you use OPLS and have calcium ions (name CA) vmd thinks they are all alpha-carbons).
> -Micholas
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of az <adam.zalewski at mail.com>
> Sent: Friday, July 24, 2015 4:26 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Chlorine in PDBs
> Hi
> Could someone enlighten me what are the "correct" (Gromacs-wise) atom
> type and PDB column numbers for a chlorine substituent in a ligand ? I
> use a MOE-written PDBs as MD input (Amber99SB), and if a chlorine is
> present, its written as CL (both letters uppercase) in the 13th and 14th
> column. Now when feeding that to acpype, the output PDB has a CL again,
> but shifted to columns 14 and 15 and with a C in the last element
> column. Seeing how this is similar to how box ions are written, I gave
> it no heed, but now PDBs saved from a completed trajectory, display the
> CL as a carbon in VMD, Chimera, or MOE. I can obviously edit that but
> I'd like to be sure if my CLs are being treated as chlorines during the MD.
> Input line:    HETATM 2166 CL   PXN     0      -7.547  -4.598 6.977
> 1.00  0.00          CL
> Post-acpype:    ATOM     26  CL  PXN Z   1      -7.547  -4.598 6.977
> 1.00  0.00           C
> Post-MD:        ATOM   2147  CL  PXN B 169       2.196   0.709 5.879
> 1.002409.13
> Cheers,
> Adam
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