Hello all I have to do MD simulation of ligand bound membrane protein in lipid bilayer. Thus I am doing tutorialfor Protein - Ligand tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html I have used following command: pdb2gmx -f 3HTB_clean.pdb -o conf.gro -water spc editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0 genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr I am getting stuck at last command. Its showing following error: Fatal error: number of coordinates in coordinate file (solv.gro, 33049) does not match topology (topol.top, 33064) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors {But when I calculate number of atom in topol.top and solv.gro it is same} When I checked above http: I got that such type of error may be due to cpp variable is not properly set in the .mdp file. But When I locate ccp in my system and add it to .mdp file. " ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run cpp =/usr/bin/cpp ; Parameters describing what to do, when to stop and what to save " Then also it showing same error. Please help me to solve this problem. I am using gromacs-4.5.5 and installed with fftw-3.3.1 . With regards Sangita Kachhap SRF BIC,IMTECH CHANDIGARH ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
