From: Jiawei Xu (jix20.forward_at_gmail.com)
Date: Fri Jan 11 2013 - 14:50:26 CST

Hi, Rajan,

Thanks very much! Your experience is very helpful.

Best,
Jiawei

On Fri, Jan 11, 2013 at 3:44 PM, Rajan Vatassery <rajan_at_umn.edu> wrote:
> 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
>> >>
>> >>
>> >>
>> >
>>
>>
>>
>

-- 
Jiawei Xu