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
--
========================================
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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