VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Dec 05 2011 - 00:07:18 CST

tim,

a new topotools 1.2 snapshot has been uploaded to my homepage at:
http://sites.google.com/site/akohlmey/software/topotools

please check, if this version solved your problems and let me/us know.

thanks,
     axel.

On Sat, Dec 3, 2011 at 7:18 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> dear tim,
>
> On Fri, Dec 2, 2011 at 12:02 PM, Timothy Sirk <tsirk_at_vt.edu> wrote:
>> apologies if this is a double post, it was dropped last time. maybe the
>> attachment was too big.
>> ======================================================
>>
>> Dear All,
>>
>> I am using topotools 1.2 with VMD 1.9 to write gromacs topology files from
>> lammps data files. With most of my datafiles this seems to work great. The
>> one exception is attached.
>>
>> When I write a top file from this particular data file, the 'atoms' section
>> is numbered incorrectly and out-of-order (see sniplet below). This numbering
>> is fatal for grompp. Can someone make a suggestion why this is happening, or
>> even try to reproduce the problem using my datafile? This is 60 molecules of
>
> i can reproduce it with my development version.
> i will look into it. johns is getting ready for the
> next release and we are currently finalizing features
> and chasing down known bugs that we want to
> have sorted out for this release.
>
>> pe at 78 atoms/molecule. I could produce a simplified system from your
>> suggestions.
>>
>> The system is a molecular crystal, where bonds are wrapped completely around
>> the box. It was orginally PCFF forcefield, but the class2 terms are stripped
>> off (BondBond, BondAngle etc) to work with topotools.
>
> this should no longer be needed with the next topotools update.
> i have implemented a fix for that just a few minutes ago.
>
>> There is also a minor issue with the number of atoms per charge group. For
>> many of my datafiles, the top output still has one too many atoms in some
>> charge groups (33 instead of 32).  Its much improved from topotools 1.1, but
>> having 32 or less would be really convenient.
>
> it works for this example, but can you please send me an input
> that still has problems? i can just arbitrarily reduce the constant
> for the maximal number of charge groups, but i'd rather understand
> the reason why you are getting the off-by-one error.
>
> more later,
>     axel.
>
>>
>> The datafile and entire .top file are attached.
>>
>> Thanks,
>>
>> Tim
>>
>>
>> [ atoms ]
>> ; nr  type  resnr residue atom cgnr charge  mass
>>      1       type1      1      RES      1      1     0.0530     1.0080
>>      2       type2      1      RES      2      1    -0.1060    12.0112
>>      3       type1      1      RES      1      2     0.0530     1.0080
>>      7       type1      1      RES      1      2     0.0530     1.0080
>>      8       type2      1      RES      2      2    -0.1060    12.0112
>>      9       type1      1      RES      1      3     0.0530     1.0080
>>     13       type1      1      RES      1      3     0.0530     1.0080
>>     14       type2      1      RES      2      3    -0.1060    12.0112
>>     15       type1      1      RES      1      4     0.0530     1.0080
>>     19       type1      1      RES      1      4     0.0530     1.0080
>>     20       type2      1      RES      2      4    -0.1060    12.0112
>>     21       type1      1      RES      1      5     0.0530     1.0080
>>     25       type1      1      RES      1      5     0.0530     1.0080
>>     26       type2      1      RES      2      5    -0.1060    12.0112
>>     27       type1      1      RES      1      6     0.0530     1.0080
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA. 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.