[gmx-users] Unnatural amino acid problems

Ashutosh Jogalekar ajogale at emory.edu
Thu Apr 20 18:04:49 CEST 2006

Hello Mark
Thanks for your comments. I realise that putting in zeros would not  
give me a good model. That's why I am putting in parameters in  
the .top file based on the atom types, which I get from the  
ffoplsaabon.itp file. But the distortion still persists, and in fact  
sometimes gets worse (at least visually), which is bizarre. I can  
only think of one one more thing that could be the reason; is  
the .top file formatted? So for example, if I put in the parameters  
for a dihedral, does each one of the numbers have to be exactly below  
c0,c1,c2,c3 etc.?

On Apr 20, 2006, at 12:41 AM, Mark Abraham wrote:

>> Hello
>> I am parametrizing an unnatural amino acid, phenylglycine (PHG), in
>> the OPLS FF in GROMACS. I have put in the necessary parameters in
>> the .hdb, .rtp, and the aminoacids.dat file.
>> 1. When I do grompp for the EM, I get an error saying that I have not
>> put in the appropriate parameters for the bonds, angles and
>> dihedrals.
> Well that means you haven't done it :-) Go back and compare what  
> you've
> done for PHG with other amino acids, see what is different and fix it.
>> Surprisingly, when I do put in the parameters (from the
>> ffoplsaabon.itp file), the angles, bonds, and dihedrals get even more
>> distorted, a counterintuitive observation. In fact the simulation is
>> much better off when I ignore the warnings and the program puts in
>> zeros after the required parameters in the .top file. Why is this
>> happening?
> You can't tell that your force field is a reasonable physical model by
> looking at the results on their own - you need a comparison with
> experiment. Often you can tell by looking at the results that it is
> completely wrong, however. Just putting in zeroes guarantees you a
> spurious model, whether you can recognise that from the results or  
> not.
>> Another question related to this:
>> 2. When I do parametrize a single peptide with a single PHG residue
>> and then simulate it (with zeros for the parameters in the .top
>> file), the PHG turns out fine and does not get distorted. But when I
>> simulate many PHG containing peptides, say 10 of them stacked on top
>> of and besides each other, I observe that some of the PHGs get
>> distorted while others don't. By distorted, I especially mean the
>> Halpha-Calpha-aromaticC angle, which gets distorted to almost 90 from
>> its normal value of about 109. Whatever the cause for this distortion
>> is, why is it affecting only some PHG residues and not others?
> It's a stochastic system... run it for long enough and you'll see  
> weird
> stuff everywhere.
> Mark
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