<br>Hi,<br><br>I am doing an energy minimization of my rsmall protein/ligand complex, following basic drug/enzyme complex EM steps on gromacs 4.0.4. After appending my ligand to my protein (pdb and top file) (also I created the pdb file and itp file for my ligand with dundee prodrg server), and solvating the complex (with commands, "editconf -bt" and "genbox -cp" using spc216.gro water), and running grompp once, I got to the "genion -s" step to neutralize and it gave me the fatal error "The solvent group SOL is not continuous: index[3]=2403, index[4]=2417." Also when I did the earlier grompp command, I got a bunch of warnings saying that my ligand coordinates did not match between my protein topology file and my before ionization protein pdb file...anyway here is the info below...can I be pointed in the right direction?<br>
<br>**This is the warning I got after running the following command:<br><br>grompp -f em.mdp -c BR6_b4ion.pdb -p BR6.top -o BR6_b4ion.tpr<br> (This was done after solvation of protein+ligand)<br><br>Warning: atom name 2406 in BR6.top and BR6_b4ion.pdb does not match (CAI - N)<br>
Warning: atom name 2407 in BR6.top and BR6_b4ion.pdb does not match (CAH - HAA)<br>Warning: atom name 2408 in BR6.top and BR6_b4ion.pdb does not match (OAK - CA)<br>Warning: atom name 2409 in BR6.top and BR6_b4ion.pdb does not match (N - CB)<br>
Warning: atom name 2410 in BR6.top and BR6_b4ion.pdb does not match (HAA - CAF)<br>Warning: atom name 2411 in BR6.top and BR6_b4ion.pdb does not match (CA - OAG)<br>Warning: atom name 2412 in BR6.top and BR6_b4ion.pdb does not match (CB - C)<br>
Warning: atom name 2413 in BR6.top and BR6_b4ion.pdb does not match (CAF - O)<br>Warning: atom name 2414 in BR6.top and BR6_b4ion.pdb does not match (OAG - OW)<br>Warning: atom name 2415 in BR6.top and BR6_b4ion.pdb does not match (C - HW1)<br>
Warning: atom name 2416 in BR6.top and BR6_b4ion.pdb does not match (O - HW2)<br><br>WARNING 1 [file BR6.top, line 15394]:<br> 16 non-matching atom names<br> atom names from BR6.top will be used<br> atom names from BR6_b4ion.pdb will be ignored<br>
<br><br>**This is the warning I got after the genion -s command below:<br><br>genion -s BR6_b4ion.tpr -o BR6_b4em.pdb -nname NA+ -nn 10 -g BR6_ion.log <br><br>Back Off! I just backed up BR6_ion.log to ./#BR6_ion.log.2#<br>
Reading file BR6_b4ion.tpr, VERSION 4.0.4 (single precision)<br>Using a coulomb cut-off of 0.9 nm<br>Will try to add 10 Na ions and 0 NA+ ions.<br>Select a continuous group of solvent molecules<br>Opening library file /opt/gromacs-4.0.4/share/gromacs/top/aminoacids.dat<br>
Group 0 ( System) has 23473 elements<br>Group 1 ( Protein) has 2398 elements<br>Group 2 ( Protein-H) has 1914 elements<br>Group 3 ( C-alpha) has 240 elements<br>Group 4 ( Backbone) has 720 elements<br>
Group 5 ( MainChain) has 961 elements<br>Group 6 (MainChain+Cb) has 1186 elements<br>Group 7 ( MainChain+H) has 1187 elements<br>Group 8 ( SideChain) has 1211 elements<br>Group 9 ( SideChain-H) has 953 elements<br>
Group 10 ( Prot-Masses) has 2398 elements<br>Group 11 ( Non-Protein) has 21075 elements<br>Group 12 ( ZN2+) has 2 elements<br>Group 13 ( SOL) has 21060 elements<br>Group 14 ( DRG) has 13 elements<br>
Group 15 ( Other) has 21075 elements<br>Select a group: 13<br>Selected 13: 'SOL'<br><br>-------------------------------------------------------<br>Program genion, VERSION 4.0.4<br>Source code file: ../../../src/tools/gmx_genion.c, line: 434<br>
<br>Fatal error:<br>The solvent group SOL is not continuous: index[3]=2403, index[4]=2417<br>-------------------------------------------------------<br><br>Thanks,<br>Halie Shah<br><br>