[gmx-users] g_rama problem about dihedrals

[Rebeca García Fandiño]

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
regafan at hotmail.com



 		 	   		  
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