[gmx-users] pdb2gmx

[Mark Abraham]

RAJAVARMAN.K wrote:
>  Respected sir,
> 
>                    am  working with gold cluster .am planing to simulate
> gold cluster in the presence of vacuum.but i can,t able
> to convert the pdb file into gro,top format caz of the
> following statement"  Residue '2' not found in residue
> topology database ".
> 
>                     i already gone through gromacs mailing list as well as
> gromacs manual 5 chapter.but i really don't know what
> to change in .rtp,.top files. so plz help me .am
> attaching my  error statement as well as input 
> file.already have  experience  in working with
> protein,peptides,domain.but this is first time am
> using  metal cluster ( i.e 40 atoms of gold).can u
> please kindly help me by creating gold cluster
> topology,gro file.

It's great that you've gone to the trouble of looking through some 
useful material before asking your question. It would also be good to 
capitalize relevant words and refrain from using non-standard 
abbreviations like "caz" and "plz". You're asking for free help from 
busy people, so you should follow business-like communication styles. 
Doing this shows that you care enough about your problem to communicate 
well, and thus it might be more worth our time to help you.

There's some useful background reading available here 
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database 
The problem comes when your coordinate file is using "2" in the place 
where pdb2gmx is expecting a residue name found in an .rtp file it 
already knows about. Unless you have a force field .rtp already 
installed that's suitable for gold clusters, you are probably using the 
wrong tool to generate a .top file. I'd expect to have to make one by 
hand, and there's really no other option than to sit down with Chapter 5 
of the manual and the paper that describes your force field and be 
prepared to work hard.

Mark