I've been having trouble minimizing a structure using gromacs so I decided to try using another MD app and see if I can generate a more relaxed structure. Using VMD & NAMD I was able to minimize and run MD for this structure from RCSB.ORG 1YQW.pdb. It was solvated and ionized.
I then took the last frame from a 10,000 step trajectory and exported it into a pdb file. I preped it so it was compatible with amber99sb port for gromacs read it into tleap using amebr99sb and wrote a pdb file from that Then fixed residues so it it was compatible with gromac pdb2gmx -ff amber99sb -f protein2.pdb -water spce -ignh editconf -bt triclinic -f conf.gro -d 1.0 genbox -cp out.gro -cs ffamber_tip3p.gro grompp -f em.mdp echo 13 |genion -s topol.tpr -neutral -conc 0.15 -p topol.top grompp -f em.mdp -c out.gro mdrun -s topol.tpr -v Back Off! I just backed up md.log to ./#md.log.2# Getting Loaded... Reading file topol.tpr, VERSION 4.0.5 (single precision) Loaded with Money Back Off! I just backed up traj.trr to ./#traj.trr.2# Back Off! I just backed up ener.edr to ./#ener.edr.2# Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 2.00000e+02 Number of steps = 10000 F-max = 2.97876e+06 on atom 16106 F-Norm = 2.59700e+04 Step 0, Epot=4.125301e+07, Fnorm=2.399e+04, Fmax=2.975e+06 (atom 16106) Step 1, Epot=4.111934e+07, Fnorm=2.285e+04, Fmax=2.969e+06 (atom 16106) Step 2, Epot=4.092903e+07, Fnorm=2.216e+04, Fmax=2.959e+06 (atom 16106) .... Step 127, Epot=7.765358e+06, Fnorm=1.020e+05, Fmax=2.836e+07 (atom 28298) Step 128, Epot=1.606771e+08, Fnorm=6.739e+07, Fmax=1.876e+10 (atom 10310) Step 129, Epot=5.454451e+09, Fnorm=4.339e+09, Fmax=1.179e+12 (atom 36500) There were 2 inconsistent shifts. Check your topology em.mdp parameters define = -DFLEXIBLE integrator = cg nsteps = 10000 constraints = none emtol = 200.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes table-extension = 100 ld_seed = -1 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
