From: Jiawei Xu (jix20.forward_at_gmail.com)
Date: Fri Jan 11 2013 - 14:22:13 CST

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