Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules

From: Tristan Croll (
Date: Fri Feb 21 2014 - 16:04:43 CST

Perhaps an easier way:

1. Use ParamChem to generate a topology for the new version of the molecule.

2. Rename atoms using a short VMD script. Assuming all your PDB files are in the same directory:

mkdir modified
foreach file [glob *.pdb] {
mol new $file
[atomselect top "resname XXX and name YYY"] set name <new name in ParamChem stream file>
[atomselect top all] writepdb ./modified/$file
mol delete top

You probably want to change the residue name as well to avoid confusion (making sure it matches the name in the stream file). Then call autopsf using a similar loop (look up the command line options to see how to do this - in particular how to choose your own topology files; you'll need both the CGENFF topology file and your new stream file on top of the standard protein topology file) and you should be left with a new set of ready-to-run PSF/PDB files.

This is, of course, assuming that your changed molecule is sufficiently "normal" for ParamChem (i.e. CGENFF) to give a good representation.



Tristan Croll
Faculty of Science and Technology
Institute of Health and Biomedical Engineering
Queensland University of Technology
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Kelvin Grove QLD 4059 Australia
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> On 22 Feb 2014, at 4:49 am, "Kenno Vanommeslaeghe" <> wrote:
>> On 02/21/2014 09:11 AM, Axel Kohlmeyer wrote:
>> of course, you have to look up details in the force field
>> documentation, because you may have to also change the force field
>> type and (partial) charge of neighboring atoms.
> Yeah, depending on details we haven't been given, this last part can get fairly tricky.

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