[gmx-users] Residue 'SIA' not found in residue topology database

[Maik Goette]

Right, Mark

But do you think, deleting something is the way, how to do it? ;)
Maybe it could be problematic, if this molecule is, what they want to
simulate in the protein...

Kong, a first step (maybe nothing for Newbies, thats for sure) would be
to make some QM-calculations with e.g. Gaussian or try Antechamber (?)
from the AMBER-package. After calculating reasonable partial charges,
you can try to get the LJ-Parameters and other stuff from existing
FF-entries. How to build the FF-entries, i.e. mainly an RTP-entry, one
can obtain from the manual.

Happy LEGOing

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
        mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Mark Abraham wrote:
> kong.winter wrote:
>> Hi all,
>> when I use the following command:"pdb2gmx -f 1G1T.pdb -p gr.top -o gr.gro"
>> There's a fatal error:
>> Residue 'SIA' not found in residue topology database
>>  
>> I checked the PDB file, the following details:
>> HET           SIA  C 601      20
>> HETNAM     SIA O-SIALIC ACID
>> FORMUL     2  SIA    C11 H19 N1 O9
>> ..........
>>  
>>  
>> Who knows how to solve it?
>> Any tip is appreciated, thank you very much.
> 
> This means what it says: the force field you're using doesn't have an
> entry for residue SIA, which is apparently sialic acid. If you want to
> simulate with this molecule in the system, you'll need to develop a
> topology for it (and maybe parameters - this is not encouraged for
> newcomers), and put that into the .rtp file (read chapter five).
> Otherwise, delete it from your .pdb file.
> 
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> .
>