Hi,
On Thu, Mar 3, 2016 at 1:16 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
> 1. I get warnings such as the one below. Are these a matter of concern?
> Warning: Using carbon SA parms for unknown atom 3985 type IP
> Warning: Using carbon SA parms for unknown atom 3986 type IP
> etc etc etc
This just means that the LCPO algorithm implemented in cpptraj doesn't
have specific parameters for the 'IP' atom type, so it defaults to
carbon parameters. The 'IP' atom type is an old one for sodium ions I
think - you may not want ions included in the calculation, so you can
strip them out beforehand.
>
> 2. For Lysine specifically I also get negative values. Example below? Any explanation for this?
>
> #Frame IntRes
> 1 24.9420
> 2 -49.4338
The LCPO algorithm is a very approximate one that estimates exposed
atom surface area from overlaps of spheres, and overlaps of
neighboring spheres. Depending on how the spheres overlap you can get
negative numbers; this was even noted in the original publication
(Weiser et al, J Comp Chem, 1999, V20, 2, p.217-230):
"The LCPO method occasionally produces negative accessible atomic
areas for atoms that are buried or nearly so."
It's just one of the things that comes along with the LCPO method. You
could use the 'datafilter' command to generate a set you can use to
filter out the negative values if you want:
surf Y222 :222
run
datafilter Y222 min 0.0 max 9999.0 name Filter_Y222
newY222 = Y222 * Filter_Y222
writedata newY222.dat newY222
That should zero out all surface areas with negative values. May or
may not be useful to you. Hope this helps,
-Dan
> 3 30.4749
> 4 13.7210
> 5 7.3940
> 6 25.5915
> 7 56.4796
> 8 -4.0526
> 9 22.3337
> 10 36.1574
> 11 26.7103
> 12 -14.6038
> 13 -38.5211
> 14 -55.6442
> 15 -68.9516
> 16 -47.4363
>
> etc etc.
>
>> On 3 Mar 2016, at 16:30, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> Hi,
>>
>> I don't think you can get what you want with the 'molsurf' command.
>> What it does is calculate the Connolly surface area of atoms specified
>> by <mask>, *not* the contribution of the atoms in <mask> to the
>> overall surface area. So the surface area of a single amino acid is
>> going to be pretty similar between different systems.
>>
>> You could try using the 'surf' command instead, which does actually
>> calculate the contribution of atoms in <mask> to the overall surface
>> area. It uses the less accurate LCPO algorithm, but for the sake of
>> comparing different systems it's probably OK as long as no large-scale
>> conformational changes are occurring.
>>
>> -Dan
>>
>> On Wed, Mar 2, 2016 at 2:58 PM, George Tzotzos <gtzotzos.me.com> wrote:
>>> I’ve been trying to work out the effect of ligand binding on homodimer formation. I’m dealing with 2 X-ray structures involving the same receptor bound to two different ligands.
>>>
>>> The ligands bind on the homodimer interface (one per subunit). The subunit main cavity is occupied by serendipitous ligands.
>>>
>>> I performed explicit solvent MD simulations of the dimer complexes in which the serendipitous ligands were stripped. The starting coordinates and conformations of the biological ligands were as per X-ray model. I also performed two separate MD simulations (a) dimer without any ligands (serendipitous or biological) and (b) monomer without any ligands.
>>>
>>> I used cpptraj molsurf to obtain the SASAs of the dimer interface residues. A typical example of a cpptraj input is:
>>>
>>> parm complex_solv.prmtop
>>> trajin prod_0-100ns.nc 1 10000 200
>>> molsurf IntRes :71 out Val71.dat
>>>
>>> The process was repeated for each interface residue for (1) monomer stripped of ligands; (2) dimer stripped of ligands; (3) dimer with ligand_1; (4) dimer with ligand_2
>>>
>>> The dimer interface consists of 28 residues.
>>>
>>> For all residues I obtained the same SASA. Typical examples are shown below.
>>>
>>>
>>> Val71
>>> His72
>>> Leu73
>>> Glu74
>>> His77
>>> monomer_apo
>>> 129.926556
>>> 154.186386
>>> 148.421838
>>> 142.796564
>>> 154.709454
>>> dimer_apo
>>> 129.384386
>>> 154.215862
>>> 148.084478
>>> 143.101678
>>> 153.807794
>>> dimer_deet
>>> 130.021954
>>> 154.398068
>>> 149.21626
>>> 143.135464
>>> 154.704514
>>> dimer_6MH
>>> 129.644992
>>> 154.301966
>>> 149.275882
>>> 143.195312
>>> 154.090458
>>>
>>> I find these results hard to explain unless the above input script is wrong.
>>>
>>> Any suggestions would be most welcome
>>>
>>> Regards
>>>
>>> George
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Mar 04 2016 - 14:30:04 PST
