Wow, thanks a lot, it works!
Nobox, Reading that part of the ptraj manual would have actually helped, ehm!
Could you comment shortly on my parameters: igb = 5, gbsa = 2 does it make sense with the afore mentioned
run parameters (ntb=2/ntp=1 ...) or are there possible pitfalls involved?
Otherwise, big thanks!
André
On 09.10.2012, at 21:26, Jason Swails wrote:
> On Tue, Oct 9, 2012 at 6:35 PM, "André C. Stiel" <
> andre.stiel.tuebingen.mpg.de> wrote:
>
>> Thanks Jason for the swift reply and obviously for parmed.py...
>> I done as told, and it kind of works out... I still have one problem, very
>> high vdw and internal energies.
>> Let me sum up (for the benefit of others) what I did:
>>
>> I have a trajectory done with explicit solvent, and now I want to extract
>> single residue energies from
>> the trajectory. This doesn´t seem to work with the explicit solvent since
>> I have to use GB.
>>
>> So, thanks to Jason, I went this way of preparing my files:
>> 1. create a water and ion stripped .mdcrd and .inpcrd with ptraj
>> 2. create a equally stripped .prmtop using parmed.py (only in
>> AmberTools 12 I figured out ;-)
>>
>> This works out fine. Now I do the energy calculation using:
>>
>> #decompose energy on a per-residue basis on the trajectory
>> &cntrl
>> imin = 5, igb = 5, gbsa = 2,
>> ntx = 1, maxcyc = 1,
>> ntc = 1, ntf = 3,
>> ntb = 0, ntp = 0,
>> ntwe = 0, ntpr = 500, ntwx=1,
>> cut = 1000.0, idecomp = 1,
>> /
>> Residues to print
>> RES 1 227
>> END
>> END
>>
>> What I get is the following. The first frame minimization values look all
>> reasonable:
>>
>> resid |internal |vdw |eel |pol |sas
>> ============================================================
>> TDC 1 97.818 -4.235 -250.591 72.307 180.515
>> TDC 2 71.769 -4.982 -64.649 -3.288 4.889
>> TDC 3 88.488 -7.834 -50.514 -91.865 60.060
>> TDC 4 91.894 -5.629 -45.914 -97.714 113.038
>> TDC 5 61.024 -6.938 -62.792 -4.081 70.127
>>
>> But in the second frame and following, the internal and vdw jump up to
>> unreasonable high values (the original trajectory itself was stable):
>>
>> resid |internal |vdw |eel |pol |sas
>> ============================================================
>> TDC 1 1619.028 1018.080 -82.695 9.640 292.780
>> TDC 2 1809.027 46.723 -47.603 -2.444 10.724
>> TDC 3 57146.677 5799.336 21.396 -87.840 36.338
>> TDC 4 26555.148 ********* 254.986 -146.093 96.970
>> TDC 5 ********* 44964.405 -18.199 -22.389 83.803
>>
>> I tried around a little bit with the different igb types (i come to
>> understand for 5 i would have to change PBradii), gbsa and the
>> cut/rgbmax values.... to no avail, I always get this hight numbers. Might
>> it be the problem that my original calculation used ntb=2/ntp=1?
>> Or are there other strange things at work here?
>>
>> Does somebody have suggestions?
>>
>
> When you use the "trajout" command in ptraj (or cpptraj) to strip out the
> solvent, add the "nobox" command. What is happening, I think, is that the
> first 3 coordinates that sander tries to extract from the second frame are
> actually the box coordinates of the first frame. After which every atom is
> 'one' index off, with the first atom having stupid coordinates (i.e., the
> box lengths).
>
> This will lead to huge bond energies as well as steric clashes.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Oct 09 2012 - 14:00:02 PDT
