From: Rajan Vatassery (rajan_at_umn.edu)
Date: Fri Jan 11 2013 - 14:44:39 CST

Hi Jiawei,
        It has been a while since I had problems with the CGenFF style atom
types, but I seem to recall some problem with VMD writing these long
atom types to new PSFs (via "writepsf"). I can't remember what happened,
but this was the reason that I switched to 3 letter atom types.
        As pertains to NAMD, I didn't notice any problems shifting the columns
over, and I think I ran about a dozen simulations this way. If the NAMD
code didn't recognize the atom types that I had in my PSF, then it
quickly let me know with a fatal error. This is to say that, as far as I
can tell, if NAMD doesn't give you a fatal error, it has assigned the
correct parameters to the correct atom types.

Rajan

On Fri, 2013-01-11 at 15:22 -0500, Jiawei Xu wrote:
> Hi, Rajan,
>
> Thanks very much for your kind help. I agree with you that modifying
> the atom types is a method. In fact, I did what you suggested and 5
> characters are fine for both VMD and NAMD.
>
> If we really want to keep the atom type as same as CGenFF, the way I
> mentioned in my poster (move the whole atom type one column left in
> the psf file) works for VMD. But I am not sure if NAMD is happy for it
> or not.
>
> Thanks.
>
> Jiawei
>
> On Fri, Jan 11, 2013 at 3:05 PM, Rajan Vatassery <rajan_at_umn.edu> wrote:
> > 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
> >>
> >>
> >>
> >
>
>
>