On Wed, Mar 13, 2013 at 1:54 PM, Chiara Pallara <chiara.pallara.bsc.es>wrote:
> Hi,
> /I have a protein/Mg-ATP structure and I'm trying to calculate //the
> binding free energy of this protein-cofactor system.
> //My input is:
>
> &general
> // strip_mask=:WAT:Cl-:Cs+:IB:K+:Li+:Na+:Rb+,
> startframe=1, endframe=5, interval=1,
> verbose=1,
> /
> &gb
> igb=5, saltcon=0.100,
> /
>
> The calculation run until the end but the results are really senseless.
> The .pdb files for Ligand, Rec and Complex are like this
> MODEL 1
> ATOM 1 HH31 ACE 1 -nan -nan -nan 0.00 0.00
> ATOM 2 CH3 ACE 1 -nan -nan -nan 0.00 0.00
> ATOM 3 HH32 ACE 1 -nan -nan -nan 0.00 0.00
> ATOM 4 HH33 ACE 1 -nan -nan -nan 0.00 0.00
> ATOM 5 C ACE 1 -nan -nan -nan 0.00 0.00
> ATOM 6 O ACE 1 -nan -nan -nan 0.00 0.00
> ATOM 7 N GLU 2 -nan -nan -nan 0.00 0.00
> ATOM 8 H GLU 2 -nan -nan -nan 0.00 0.00
> ATOM 9 CA GLU 2 -nan -nan -nan 0.00 0.00
> ATOM 10 HA GLU 2 -nan -nan -nan 0.00 0.00
> ATOM 11 CB GLU 2 -nan -nan -nan 0.00 0.00
> ATOM 12 HB2 GLU 2 -nan -nan -nan 0.00 0.00
>
> And in the "FINAL_RESULTS_MMPBSA.dat", I found...
>
> GENERALIZED BORN:
>
> Complex:
> Energy Component Average Std. Dev. Std. Err.
> of Mean
>
> -------------------------------------------------------------------------------
> EGB -66427.3241 0.0000 0.0000
>
> G gas 0.0000 0.0000 0.0000
> G solv -66427.3241 0.0000 0.0000
>
> TOTAL -66427.3241 0.0000 0.0000
>
>
> Receptor:
> Energy Component Average Std. Dev. Std. Err.
> of Mean
>
> -------------------------------------------------------------------------------
> EGB -64081.8425 0.0010 0.0004
>
> G gas 0.0000 0.0000 0.0000
> G solv -64081.8425 0.0010 0.0004
>
> TOTAL -64081.8425 0.0010 0.0004
>
>
> Ligand:
> Energy Component Average Std. Dev. Std. Err.
> of Mean
>
> -------------------------------------------------------------------------------
> EGB -2345.4816 0.0000 0.0000
>
> G gas 0.0000 0.0000 0.0000
> G solv -2345.4816 0.0000 0.0000
>
> TOTAL -2345.4816 0.0000 0.0000
>
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err.
> of Mean
>
> -------------------------------------------------------------------------------
> VDWAALS 0.0000 0.0000 0.0000
> EEL 0.0000 0.0000 0.0000
> EGB 0.0000 0.0000 0.0000
> ESURF 0.0000 0.0000 0.0000
>
> DELTA G gas 0.0000 0.0000 0.0000
> DELTA G solv 0.0000 0.0000 0.0000
>
> DELTA TOTAL 0.0000 0.0000 0.0000
>
>
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> /
> Can anyone tell me what i'm doing wrong? or some suggestion?
>
You haven't provided enough information to diagnose what (if anything) is
going wrong. It would also help to know some common pitfalls that you
checked (e.g., are the topology files and trajectory files generated by
MMPBSA.py compatible? If you visualize them together does it look correct?)
It also appears that you haven't shown us the full output files (but maybe
you have). There are also random slashes that appear in your email, and
I'm not sure why. If the // is present in your input file right after your
&general section, those need to be removed.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Mar 13 2013 - 14:30:03 PDT
