VMD-L Mailing List

From: Donovan B.T. (B.T.Donovan_at_soton.ac.uk)
Date: Wed May 16 2012 - 08:54:59 CDT

Hi All

In my efforts to get charge information into VMD, I use a PSF file generated from a .gro file which I then skin out to contain the right charge information from a script that I have written. Hence I generate <AutoPSF.psf> from AutoPSF. I can then get the correct charge information into VMD and then I use a TCL/TK script to perform my analyses.

Usually I have no issues with this, but on some new trajectories produced by another group the PSF format generated by AutoPSF has very different format from that expected in that the residue names are very different indeed from that in the .gro file. In fact there seems not to be the right number of atoms in each molecule and there is not the

In the .gro file, I have the following:

    1CHOL C1 1 3.201 3.368 8.649 0.2640 -0.1923 -0.5491
    1CHOL C2 2 3.236 3.318 8.790 0.4547 0.0812 -0.4976
    1CHOL C3 3 3.342 3.405 8.858 0.1900 -0.0133 0.0368
    1CHOL C4 4 3.476 3.391 8.785 -0.0486 -0.3611 -0.3401
    1CHOL C5 5 3.541 3.253 8.792 0.2187 -0.2329 -0.3147
    1CHOL O6 6 3.669 3.264 8.729 0.2166 -0.0700 -0.2920
....

but in the AutoPSF generated o/p file I get the following:

    1 O1 1 CHOL N NTL -0.600000 14.0070 0
       2 O1 1 CHOL C1 CTL2 -0.100000 12.0110 0
       3 O1 1 CHOL C2 CTL5 -0.350000 12.0110 0
       4 O1 1 CHOL C3 CTL5 -0.350000 12.0110 0
       5 O1 1 CHOL C4 CTL5 -0.350000 12.0110 0
       6 O1 1 CHOL H11 HL 0.250000 1.0080 0
...

I don't get the right residue names copied from the .gro file into the autogenerated .psf file. The names are completely different. I have no idea where this is going wrong or how to do the mapping,

Thanks

Brett