Hello, I have an old trajectory simulated using the Charmm force field and I would like to get the Phi/Psi dihedral combinations as a function of time, using g_raman. I am using a single pdb to start with. I created a topology for this pdb using:
pdb2gmx -f protein.pdb -o protein_gmx.pdb -p topol.top (and selecting 8: CHARMM27 all-atom force field (with CMAP) - version 2.0beta) Then, I generated a .tpr file using grompp and I used the g_raman tool: g_rama -f protein_gmx.gro -s topology.tpr -o rama.xvg I get a file called rama.xvg with a pair value for each residue (except for the terminal ones), that is something like: @ s0 symbol 2 @ s0 symbol size 0.4 @ s0 symbol fill 1 -83.2716 85.9943 LYS-2 -89.0885 36.4162 ILE-3 -91.7006 61.4224 GLY-4 (...) But I get a lot of messages saying: Reading file topology.tpr, VERSION 4.5 (single precision) Found 166 phi-psi combinations Dihedral around 24,26 not found in topology. Using mult=3 Dihedral around 26,44 not found in topology. Using mult=3 Dihedral around 46,48 not found in topology. Using mult=3 Dihedral around 48,63 not found in topology. Using mult=3 Dihedral around 65,67 not found in topology. Using mult=3 (...) Dihedral around 2526,2528 not found in topology. Using mult=3 Dihedral around 2528,2544 not found in topology. Using mult=3 Dihedral around 2546,2548 not found in topology. Using mult=3 Dihedral around 2548,2551 not found in topology. Using mult=3 I have seen there are other people in the Gromacs list that have asked about this question, but I could not find any help from the answers there. Any help will be very appreciated! Thanks a lot in advance, Rebeca Garcia Universidad de Santiago de Compostela Spain [email protected]
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