[gmx-users] peptide & bilayer sims

[kia balali]

Dear Dr. Lindahl/Van Der Spoel/Feenstra,

Sorry to be a pain again, but the protocol I emailed in to be checked over 
was with SPC in the system....without solvent and using the ffgmx2 
forcefield....it not surprsingly crashes. My Mistake....apologies

I used the -ter option to cap the N terminus of my peptide with ACE..and put 
a COO- on the c terminus...I put in a Na+ counterion near the C teminus and 
placed 3 Cl- counter ions near the LYS residues to counteract the peptides 
+3 ve...

However grompp gives me three warnings on angles and 1 on proper 
dihedrals......I looked up ffgmx2bon.itp...the corresponding angles and 
dihedral dont exist... shall i put them in manually with the closest/most 
similar value from another angle/dihedral...? or would you recommend another 
method??

Do either of you have any suggestions on how I could decrease the potential 
energy of my peptide without solvating it? DMSO...could that be an 
option??????

Thanks in advance....

best wishes

Kia




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