[gmx-users] request for dihedral PMF test system or complete alanine dipeptide topology file
David Mobley
dmobley at gmail.com
Wed Apr 25 23:12:29 CEST 2007
Chris,
I'll have to assume you know what you're doing with using impropers to
calculate PMFs. I've done this using the dihedral restraints code.
Have you double-checked that? That's the first place I would look.
Otherwise, I don't have a great test system for you.
David
On 4/25/07, Chris Neale <chris.neale at utoronto.ca> wrote:
> Does anybody have a good test system for reproducing the PMF about a
> dihedral? I believe that my procedure is correct, and I have
> successfully reproduced a 1d dihedral PMF for a 4 atom chain system
> simulated in the absence of nonbonded interactions.
>
> However, my results using an oplsaa interpretation of the alanine
> dipeptide ACE-ALA-NAC disagree with the literature both in unconstrained
> runs and in a 2D phi-psi PMFs. For example my unconstrained runs of 25ns
> only sample beta space and my PMF shows a 6kcal/mol barrier for
> transition over psi from beta to alphaR. On the other hand
> (Hu,Elstner,Hermans,Proteins 2003) show that 6ns is enough to
> significantly sample both Beta and alphaR space and (Ponder,Case,
> Adv.Prot.Chem 2003) indicates that the barrier for this beta-alphaR
> transition should be between 1.5 and 2 kcal/mol.
>
> If somebody has a good test system that would be greatly appreciated. I
> am also including my alanine dipeptide topology file, but I am fairly
> sure that it is correct. The only thing that I still question is the
> difference between the C-N-CT-HC dihedral parameters (c-terminal in
> alanine dipeptide) and C-N-CT_2-HC dihedral parameters (involved where
> i+1 is an amino acid residue and not NAC) in ffoplsaabon.itp. However, I
> have tested the system while modifying C-N-CT-HC to all zeroes and it
> does not change the gross morphology of my results.
>
> In addition I have defined the following types at the beginning of my
> .top file to correspond to the CT=CT_2 case as I have previously posted
> here:
> http://www.gromacs.org/pipermail/gmx-users/2006-September/023875.html.
> As a further test I have generated PMFs without the inclusion of these
> additional parameters, allowing them to default to all zeroes and it
> does not change the gross morphology of my results.
> [ dihedraltypes ]
> CT C N CT_2 3 30.28798 -4.81160 -25.47638
> 0.00000 0.00000 0.00000 ; peptide - V1 changed to 2.3
> CT_2 C N CT 3 30.28798 -4.81160 -25.47638
> 0.00000 0.00000 0.00000 ; peptide - V1 changed to 2.3
>
> Before moving on to my .itp file, here are a couple of other points of
> interest for anybody embarking on a dihedral PMF determination:
> (i) g_chi uses non-standard dihedrals, use g_rama instead.
> (ii) the default xtc_precision=1000 may not be large enough to get the
> most out of your data. The default value here is fine for distances, but
> the precision in a dihedral will be less than the precision in the
> coordinates when the dihedral is calculated from the saved coordinates.
>
> Many thanks,
> Chris.
>
> $cat alaninedipeptide.itp
>
> [ moleculetype ]
> ; Name nrexcl
> dialanine 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 opls_135 1 ACE CH3 1 -0.18 12.011 ;
> qtot -0.18
> 2 opls_140 1 ACE HH31 1 0.06 1.008 ;
> qtot -0.12
> 3 opls_140 1 ACE HH32 1 0.06 1.008 ;
> qtot -0.06
> 4 opls_140 1 ACE HH33 1 0.06 1.008 ;
> qtot 0
> 5 opls_235 1 ACE C 2 0.5 12.011 ;
> qtot 0.5
> 6 opls_236 1 ACE O 2 -0.5 15.9994 ;
> qtot 0
> 7 opls_238 2 ALA N 3 -0.5 14.0067 ;
> qtot -0.5
> 8 opls_241 2 ALA H 3 0.3 1.008 ;
> qtot -0.2
> 9 opls_224B 2 ALA CA 3 0.14 12.011 ;
> qtot -0.06
> 10 opls_140 2 ALA HA 3 0.06 1.008 ;
> qtot 0
> 11 opls_135 2 ALA CB 4 -0.18 12.011 ;
> qtot -0.18
> 12 opls_140 2 ALA HB1 4 0.06 1.008 ;
> qtot -0.12
> 13 opls_140 2 ALA HB2 4 0.06 1.008 ;
> qtot -0.06
> 14 opls_140 2 ALA HB3 4 0.06 1.008 ;
> qtot 0
> 15 opls_235 2 ALA C 5 0.5 12.011 ;
> qtot 0.5
> 16 opls_236 2 ALA O 5 -0.5 15.9994 ;
> qtot 0
> 17 opls_238 3 NAC N 6 -0.5 14.0067 ;
> qtot -0.5
> 18 opls_241 3 NAC H 6 0.3 1.008 ;
> qtot -0.2
> 19 opls_242 3 NAC CH3 7 0.02 12.011 ;
> qtot -0.18
> 20 opls_140 3 NAC HH31 7 0.06 1.008 ;
> qtot -0.12
> 21 opls_140 3 NAC HH32 7 0.06 1.008 ;
> qtot -0.06
> 22 opls_140 3 NAC HH33 7 0.06 1.008 ;
> qtot 0
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 3 1
> 1 4 1
> 1 5 1
> 5 6 1
> 5 7 1
> 7 8 1
> 7 9 1
> 9 10 1
> 9 11 1
> 9 15 1
> 11 12 1
> 11 13 1
> 11 14 1
> 15 16 1
> 15 17 1
> 17 18 1
> 17 19 1
> 19 20 1
> 19 21 1
> 19 22 1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 8 1
> 1 9 1
> 2 6 1
> 2 7 1
> 3 6 1
> 3 7 1
> 4 6 1
> 4 7 1
> 5 10 1
> 5 11 1
> 5 15 1
> 6 8 1
> 6 9 1
> 7 12 1
> 7 13 1
> 7 14 1
> 7 16 1
> 7 17 1
> 8 10 1
> 8 11 1
> 8 15 1
> 9 18 1
> 9 19 1
> 10 12 1
> 10 13 1
> 10 14 1
> 10 16 1
> 10 17 1
> 11 16 1
> 11 17 1
> 12 15 1
> 13 15 1
> 14 15 1
> 15 20 1
> 15 21 1
> 15 22 1
> 16 18 1
> 16 19 1
> 18 20 1
> 18 21 1
> 18 22 1
>
> [ angles ]
> ; ai aj ak funct c0 c1
> c2 c3
> 2 1 3 1
> 2 1 4 1
> 2 1 5 1
> 3 1 4 1
> 3 1 5 1
> 4 1 5 1
> 1 5 6 1
> 1 5 7 1
> 6 5 7 1
> 5 7 8 1
> 5 7 9 1
> 8 7 9 1
> 7 9 10 1
> 7 9 11 1
> 7 9 15 1
> 10 9 11 1
> 10 9 15 1
> 11 9 15 1
> 9 11 12 1
> 9 11 13 1
> 9 11 14 1
> 12 11 13 1
> 12 11 14 1
> 13 11 14 1
> 9 15 16 1
> 9 15 17 1
> 16 15 17 1
> 15 17 18 1
> 15 17 19 1
> 18 17 19 1
> 17 19 20 1
> 17 19 21 1
> 17 19 22 1
> 20 19 21 1
> 20 19 22 1
> 21 19 22 1
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> 2 1 5 6 3
> 2 1 5 7 3
> 3 1 5 6 3
> 3 1 5 7 3
> 4 1 5 6 3
> 4 1 5 7 3
> 1 5 7 8 3
> 1 5 7 9 3
> 6 5 7 8 3
> 6 5 7 9 3
> 5 7 9 10 3
> 5 7 9 11 3
> 5 7 9 15 3
> 8 7 9 10 3
> 8 7 9 11 3
> 8 7 9 15 3
> 7 9 11 12 3
> 7 9 11 13 3
> 7 9 11 14 3
> 10 9 11 12 3
> 10 9 11 13 3
> 10 9 11 14 3
> 15 9 11 12 3
> 15 9 11 13 3
> 15 9 11 14 3
> 7 9 15 16 3
> 7 9 15 17 3
> 10 9 15 16 3
> 10 9 15 17 3
> 11 9 15 16 3
> 11 9 15 17 3
> 9 15 17 18 3
> 9 15 17 19 3
> 16 15 17 18 3
> 16 15 17 19 3
> 15 17 19 20 3
> 15 17 19 21 3
> 15 17 19 22 3
> 18 17 19 20 3
> 18 17 19 21 3
> 18 17 19 22 3
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3
> 1 7 5 6 1 improper_O_C_X_Y
> 5 9 7 8 1 improper_Z_N_X_Y
> 9 17 15 16 1 improper_O_C_X_Y
> 15 19 17 18 1 improper_Z_N_X_Y
>
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