VMD-L Mailing List

From: Rajan Vatassery (rajan_at_umn.edu)
Date: Fri Jan 11 2013 - 14:05:47 CST

Jiawei,
        I had some problems with the CGenFF parameter sets as well, and the
best way to get around this was to change all the atom types to
something with only 3 characters. For example, HGR61 is now H61 in both
my parameter file and my PSF. For a while I just simply added a column
so that the atom type column wouldn't run into the next column, and I
don't believe this caused any errors in NAMD, but VMD didn't like it.
Here's a quick description from a while back when I had the information
more fresh in my head:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/3864.html

        The easiest way to do this is to, from the start, use 3-character atom
types. I agree that the information in the manual/tutorials are not
comprehensive regarding the structure of the PSF, but the source code is
freely available (which is really the best bet if you have time).

Good luck,

Rajan

On Fri, 2013-01-11 at 12:28 -0500, Jiawei Xu wrote:
> Hi,
>
> That is because you have atom type longer than 5 characters in PSF
> file. Thus VMD read a wrong charge. Please see the following question
> I have posted several days ago.
>
> Hi,
>
> In the psf file, the element type, such as CG2R61 and HGR61, usually
> from column 30 as following:
>
> 25521 D1 1 PFL CG CG2R61 -0.230000 12.0110 0
>
> 25522 D1 1 PFL HG HGR61 0.140000 1.0080 0
>
> However, since CG2R61 is a little bit longer name, when calculate the
> charge on CG as following in VMD, it gave a wrong number:
>
>
> set charge [vecsum [$cg get charge]]
>
> CG2R61: 1.0 # not -0.23 but read the number "1" in "CG2R61",
> reading the character on column 35.
>
> HGR61 : 0.14
>
>
>
> If modifying the psf file as the following, (move CG2R61 one column
> left) it gave the right charge for CG CG2R61. However, the element
> type of CG2R61 start from column 29 now (no as usual).
>
>
> 25521 D1 1 PFL CG CG2R61 -0.230000 12.0110 0
>
> 25522 D1 1 PFL HG HGR61 0.140000 1.0080 0
>
>
> set charge [vecsum [$cg get charge]]
>
> CG2R61: -0.23
>
> I am wondering if it will cause problem in NAMD calculations?
> I am wondering if there is a better way to solve this problem.
> I am wondering where I can find the explanation of the EXACT format of
> psf file. By the way, the content in
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node21.html
> is not enough.
>
>
> Thanks very much!
>
>
> On Fri, Jan 11, 2013 at 3:06 AM, Shaherin Basith <shaherinb_at_gmail.com> wrote:
> > Dear VMD support team,
> >
> > I'm trying to neutralize the protein-DNA complex system using 'Autoionize'
> > plugin in VMD.
> >
> > The plugin calculates:
> >
> > System net charge before adding ions: -20.81999099254608e.
> > Ions to be placed: 20 SOD
> > System net charge after adding ions: -0.8199909925460815e.
> >
> > Then an error message reads as follows:
> > "System has a non-integer total charge. There was likely a problem in the
> > process of building it."
> >
> > The.pdb and .psf files were created using VMD 1.9.1.
> >
> > Due to this error, when I subjected the ionized system for NAMD simulation
> > it showed strange energy levels and the program eventually stopped as
> > "Exiting prematurely."
> > In this situation, I'm not sure if the net charge of system caused the
> > failure of equilibration with NAMD.
> >
> > Please help me in this regard.
> >
> > Thanking you in anticipation.
> >
> > Regards,
> > --
> > Shaherin Basith
> > Phd Student
> > Systems Biology lab
> > Ajou University
> > Suwon
> > South Korea
> > e-mail: shaherinb_at_ajou.ac.kr
> > Mobile: 010-6873-1033
>
>
>