[gmx-users] make a new bond in VERSION 4.5.4

[Justin A. Lemkul]

Yulian Gavrilov wrote:
> 
> 
> Thank you!
> 
> I changed the residue names in the .pdb file to LYQ and GLQ
> 
> LYQ NZ 1 GLQ C 1 0.13 LYQ GLQ
> 
> pdb2gmx -f ubc7_94_t48_newgmx1.pdb -o processed.gro -water tip3p 
> -chainsep interactive -ignh -rtpres
> 
> 
> Program pdb2gmx, VERSION 4.5.4
> 
> Source code file: resall.c, line: 581
> 
> Fatal error:
> 
> Residue 'LYQ' not found in residue topology database
> 
> For more information and tips for troubleshooting, please check the GROMACS
> 
> website at http://www.gromacs.org/Documentation/Errors
> 
> -------------------------------------------------------
> 
> I checked http://www.gromacs.org/Documentation/File_Formats/Topology_File
> 
> But as you see from the previous mail, I included LYQ and GLQ to the 
> force field. Maybe I missed something?
> 
> 

Apparently you did not add .rtp entries for these residues.  See 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field 
for all necessary steps and be sure you've completed all of them.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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