VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jul 23 2012 - 12:42:50 CDT

On Mon, Jul 23, 2012 at 7:24 PM, satya kumar <mail2mvskumar_at_gmail.com> wrote:
> Thanks for the reply.
>
> I tried converting ,gro to .pdb format. I tried to view in VMD but the Z
> coordinate is creating an issue again. In .pdb format we have:
>
> ATOM 5231 OW OHX 2171 -5.430 -25.80010000.000 1.00 0.00
> ATOM 5232 HW1 OHX 2171 -5.100 -25.47010001.100 1.00 0.00

this is not a correctly formatted .pdb file.

axel.

> Instead of reading Z coordinate as 1000 and 10001.100, VMD is reading them
> as 000 and 0001.100. Probably there should be a white space between
> successive columns.
>
> With Regards,
> Satya.
>
>
>
> On Mon, Jul 23, 2012 at 12:46 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Mon, Jul 23, 2012 at 5:06 AM, satya kumar <mail2mvskumar_at_gmail.com>
>> wrote:
>> > Hello All,
>> >
>> > I am a VMD user, experiencing an issue with reading coordinates in VMD
>> > from
>> > a Gromacs file. Sample coordinate from GRO file is:
>> >
>> > 1OHX OW 5231 -0.543 -2.5801000.000
>> > 1OHX HW1 5232 -0.510 -2.5471000.110
>> >
>> > where the "position (in nm, x y z in 3 columns, each 8 positions with 3
>> > decimal places)". {X,Y,Z} = {-0.543, -2.580, 1000.00} and {X,Y,Z} =
>> > {-0.510,
>> > -2.547, 1000.110}. When we view in VMD, these numbers are multiplied
>> > with a
>> > factor 10 to convert to Angstrom, then in particular Z coordinates are
>> > converted to 000 and 0.110 respectively. In VMD the above coordinates
>> > taken
>> > as:
>> >
>> > {-5.429999828338623 -25.801000595092773 0.0}
>> > {-5.099999904632568 -25.47100067138672 1.100000023841858}
>> >
>> > These create problems with respect to analysis, in particular the Z
>> > coordinate. Can someone guide me to fix this issue.
>>
>> you have to fix the gromacs plugin reader to not use
>> a simple scanf() call to parse coordinates in .gro files,
>> but split the columns first and then parse the numbers.
>> same as the .pdb molfile plugin does.
>>
>> ... or you simply use a (different) file format where
>> these issues don't show.
>>
>> axel.
>>
>>
>> >
>> > Thanks,
>> > Satya.
>> >
>> >
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.