VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Apr 07 2017 - 07:58:04 CDT

This is probably because as Joao noted, there is an OFFICIAL SDS residue definition in top_all27_prot_lipid_na.inp. This raises the question — why are you reinventing the wheel on this molecules? If you wanted to use your own version, you’d at least need to add appropriate MASS lines to your topology file to make sure all the atom types are defined… but unless you have some reason to prefer the cgenff based parameters that you came up with, you’re probably better off with the one that ships with the charmm forcefields.

Thanks,
Peter

> On Apr 7, 2017, at 1:08 AM, Harish Srinivasan <harishlglk1992_at_gmail.com> wrote:
>
> Hi Peter,
>
> I am using vmd 1.9.2. Actually, it seems to work now if include cgenff_*.rtf along with the *.str files that I have used.
>
> Thanks
>
> On 7 April 2017 at 06:20, Peter Freddolino <petefred_at_umich.edu> wrote:
> Dear Harish,
> Could you please confirm the version of vmd that you are using, and the set of topology files that you have loaded? When I use your inputs with autopsf it gives correct output.
> Thanks,
> Peter
>
> > On Apr 6, 2017, at 2:37 AM, Harish Srinivasan <harishlglk1992_at_gmail.com> wrote:
> >
> > Hi,
> >
> > I am trying to construct a psf file from a given pdb file. I am using an rtf file for topology of the molecule. After the generating psf file, the autopdb file generated has a really messed up structure.
> >
> > I have attached the initial pdb & rtf files and the final generated autopdb and autopsf files here.
> >
> > What could be the reason behind this ?
> >
> > Thank you
> > Harish
> > <dodecylsulphate.rtf><dodecylsulphate2.pdb><dodecylsulphate2_autopsf.psf><dodecylsulphate2_autopsf.pdb>
>
>