Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules

From: Tristan Croll (tristan.croll_at_qut.edu.au)
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.

Cheers,

Tristan

 
 
Tristan Croll
Lecturer
Faculty of Science and Technology
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
 
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> On 22 Feb 2014, at 4:49 am, "Kenno Vanommeslaeghe" <kvanomme_at_rx.umaryland.edu> 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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