[gmx-users] peptide & bilayer sims

[David]

On Thu, 2003-03-20 at 18:40, kia balali wrote:
> 
> 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
Why do you use ffgmx2? Go for gromos96 (ffG43a1) or OPLS instead.

> 
> 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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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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