VMD-L Mailing List

From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Fri Mar 30 2012 - 14:25:06 CDT

Hi James,

        If you're familiar with Unix command tools, PDBCat can help you create properly formatted PDB files:

http://www.ks.uiuc.edu/Development/MDTools/pdbcat/

====
PDBCat can be used to manipulate and process PDB files using commonly available tools such as Perl, awk, etc.
====

                Cheers,

                Barry

On Mar 30, 2012, at 2:04 PM, Jeffrey Potoff wrote:

> Your "PDB" format is not correct. It is very strict format and if you get it wrong, you will get garbage. It's somewhat maddening because even hidden tab characters will throw it off.
>
> You can find the rules governing the PDB format here:
> http://www.wwpdb.org/docs.html
>
> It may be easiest to grab one of the PDB files from a NAMD tutorial and use that as a template to build your file.
> Regards,
> J.
>
> On 3/30/2012 12:37 PM, james Fernandez wrote:
>> Hi VMD USERS,
>> I am trying to plot some co-ordinates(points) on VMD and I used a simple format of a PDB file but its giving a wrong figure.
>> The format of the pdb file that i used is as follows,
>>
>> 8!
>> REMARK 350 BIOMOLECULE: 1
>>
>> ATOM 1 28.407 28.897 5.314 1.00 9.00
>> ATOM 2 28.238 28.590 4.518 1.00 9.00
>> ATOM 3 28.343 27.156 2.578 1.00 9.00
>> ATOM 4 24.707 24.752 0.377 1.00 9.00
>> ATOM 5 24.641 22.884 -1.74 1.00 9.00
>> ATOM 6 23.405 19.850 -3.63 1.00 9.00
>> ATOM 7 22.710 16.487 -4.12 1.00 9.00
>> ATOM 8 22.205 13.628 -5.88 1.00 9.00
>>
>> I am trying to connect these molecules through bonds i am able to connect it but the co-ordinates that are getting plotted on VMD are not accurate.
>>
>> Can someone please help me in getting these co-ordinates plotted since I am NEW to this software. I will be very thankful to you and your help will be appreciated.
>>
>> Regards
>> James
>
>
> --
> =================================================================
> Jeffrey J. Potoff jpotoff_at_wayne.edu
> Associate Professor Wayne State University
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> Detroit, MI 48202 Fax: (313)578-5815
> http://potoff1.eng.wayne.edu
> ================================================================= 

-- 
Barry Isralewitz
Theoretical and Computational Biophysics Group
3043 Beckman, University of Illinois at Urbana-Champaign
Office Phone: (217) 244-1612
email: barryi_at_ks.uiuc.edu   http://www.ks.uiuc.edu/~barryi