Negative Born radii with v(z) = 2

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ldav
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Negative Born radii with v(z) = 2

Post by ldav » Mon Aug 11, 2008 7:48 am

During MC simulations, when using the option "v(z)_mode [1=linear 2=gauss 3=exp] 2" I get the following message in the log.txt file:
Info: negative born radius (too many terms in descreening sum - use cutoff) t = 0 rbinvf = -0.00251 (ATOM: 790 HA 90 VAL) and the calculated Born radius for atoms from residue 90 given in out_born_radii.dat are:
-------------------------
ATOM RB RBINV VOL Q QB
784 CA (VAL 90) 136.3499 0.0073 0.1044 0.1400 0.1400 CT
785 C (VAL 90) 209.9815 0.0048 0.0632 0.5000 0.5000 C
786 HN (VAL 90) 15.5806 0.0642 0.3460 0.3000 0.3000 H
787 CB (VAL 90) 89.5149 0.0112 0.2181 -0.0600 -0.0600 CT
788 CG1 (VAL 90) 293.5739 0.0034 0.0153 -0.1800 -0.1800 CT
789 CG2 (VAL 90) 70.5150 0.0142 0.4241 -0.1800 -0.1800 CT
790 HA (VAL 90) -399.0489 -0.0025 0.0000 0.0600 0.0600 HC
791 HB (VAL 90) 26.0313 0.0384 0.2869 0.0600 0.0600 HC
792 HG1 (VAL 90) 298.8938 0.0033 0.0201 0.0600 0.0600 HC
793 HG2 (VAL 90) 438.5416 0.0023 0.0031 0.0600 0.0600 HC
794 HG3 (VAL 90) 138.4390 0.0072 0.0345 0.0600 0.0600 HC
795 HG4 (VAL 90) 35.3150 0.0283 0.1456 0.0600 0.0600 HC
796 HG5 (VAL 90) 515.6824 0.0019 0.0073 0.0600 0.0600 HC
797 HG6 (VAL 90) 25.3323 0.0395 0.2545 0.0600 0.0600 HC
-------------------------

After many million steps MC generated the residue 90 makes the alpha helix unwinding. If I use the exponential ("v(z)_mode 3") instead of the gaussian function, no 'Info' message is given in the log.txt file (no negative Born radii) and the helix seems stable.

martin
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Re: Negative Born radii with v(z) = 2

Post by martin » Wed Aug 13, 2008 10:23 am

- The exponential can be better at keeping helices stable, so it's fine to use it. A good combination is often to use a Gaussian for the Born and V(z) term and an exponential for the SASA term. The following works well for e.g. WALP:
born_mode [1=exp 2=gauss] 2
sasa_mode [0,1=v(z) 2=gauss 3=exp] 3
v(z)_mode [1=linear 2=gauss 3=exp] 2
gamma_born -3.0
gamma_born2 -3.0
gamma_sasa -1.5
gamma_v(z) -3.0
L [A] 15

- Negative Born radii are not a bug and the program automatically handles them. But negative Born radii usually indicate that there is something wrong with the structure.

Try doing a 'transrot scan' and see if the protein has an inserted minima. For large proteins the membrane surface tension (i.e. membrane attraction) might have to be increased, as the original value is optimized for single helices.

Good luck! :)

ldav
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Re: Negative Born radii with v(z) = 2

Post by ldav » Tue Aug 19, 2008 7:43 am

Thanks Martin,

In fact I used a decreased membrane surface tension during the simulation, as well as a decreased length membrane to mimick POPC and otherwise the same values for the remaining parameters:
sigma_membrane -0.03
born_mode [1=exp 2=gauss] 2
sasa_mode [0,1=v(z) 2=gauss 3=exp] 3
v(z)_mode [1=linear 2=gauss 3=exp] 2
gamma_born -3.0
gamma_born2 -3.0
gamma_sasa -1.5
gamma_v(z) -3.0
L [A] 13
Among the different runs I performed, the only way I could get a stable system (no unwinding helix) was to use 'v(z)_mode [1=linear 2=gauss 3=exp] 2'.

I am not sure I understand what I would get with a 'transrot scan'. As the simulation with 'V(z) = 2' is stable, it seems that the system is in an acceptable minimum or?

martin
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Re: Negative Born radii with v(z) = 2

Post by martin » Fri Aug 29, 2008 8:09 am

The transrot scan will take your protein structure and rotate and translate it through the membrane (zmin->zmax, adjust dz, dtheta and dphi). It will then print out the insertion surface. This will tell you if the native state of the protein sits stably in the membrane (indicated by TST atoms in the global_minimum.pdb). If it doesn't you can increase the membrane surface tension until it inserts properly.

Hope this helps!

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