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Hello friends, I am trying to simulate a protein of 36 residues (HBD1) in water . Since my protein has net charge of +4 I had to neutralize it by adding 4 chlorine ions using ' genion'. After that I edited the .top file to add the required "ions.itp" and also reduced the number of SOL molecules by 4 in the [ molecules ] line and added one line for Cl 4 to complete the top file. After this when I run the grompp program with the new pdb file containing the ions. However it is not able to recognize the Cl ions ... The following are the sequence of commands I give: pdb2gmx -f HBD1pr.pdb -o HBD1prn.pdb -p HBD1pr.top -ignh editconf -f HBD1prn.pdb -o HBD1pr_box.gro -c -d 0.6 genbox -cp HBD1pr_box.gro -cs spc216.gro -o HBD1pr_b4em.gro -p HBD1pr.top grompp -f em.mdp -c HBD1pr_b4em.gro -p HBD1pr.top -o HBD1pr_em.tpr genion -s HBD1pr_em.tpr -o HBD1pr_ion.pdb -nname Cl -nn 4 -nq -1 -random I edit the HBDpr.top for including the "ions.itp" and modify the number of SOL molecules and also add a line for Cl ions. then delete the HBD1pr_em.tpr file to create a new tpr file. rm HBD1pr_em.tpr grompp -f em.mdp -c HBD1pr_ion.pdb -p HBD1pr.top -o HBD1pr_em.tpr the error is : Back Off! I just backed up mdout.mdp to ./#mdout.mdp.41# Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar checking input for internal consistency... calling /lib/cpp... processing topology... Generated 135 of the 1081 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_B 1 Excluding 2 bonded neighbours for SOL 1366 Cleaning up temporary file grompp013645 Fatal error: No such moleculetype Cl Where am I going wrong I am not able to figure out. Has anybody come across such problem...please help with suggesions sharada |
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