Hi Dan,
Many thanks. Much appreciated.
I’m now running surf and came across two issues:
1. I get warnings such as the one below. Are these a matter of concern?
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: '4fqt_solv.prmtop', 48516 atoms, 15106 res, box: Trunc. Oct., 14858 mol, 14838 solvent, 50 frames
INPUT TRAJECTORIES:
0: 'prod_0-100ns.nc' is a NetCDF AMBER trajectory, Parm 4fqt_solv.prmtop (Trunc. Oct. box) (reading 50 of 10001)
Coordinate processing will occur on 50 frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '4fqt_solv.prmtop' (1 actions):
0: [surf IntRes :222 out Tyr222.dat]
LCPO surface area will be calculated for 21 atoms.
21 solute atoms.
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
2. For Lysine specifically I also get negative values. Example below? Any explanation for this?
#Frame IntRes
1 24.9420
2 -49.4338
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
>>
>>
>>
>>
>>
>> _______________________________________________
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>> 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
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Received on Thu Mar 03 2016 - 12:30:04 PST
