Dear Devrani,
This is not the best pdb structure around :-( For starters it is only at 2.5
angstrom resolution. Then if you read the headers:
REMARK 400 COMPOUND
REMARK 400 DELETION MUTANT LEU 127.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 274
REMARK 465 GLU A 275
REMARK 465 VAL A 276
REMARK 465 GLU A 277
REMARK 465 ASP A 278
REMARK 465 GLU A 279
REMARK 465 SER A 280
REMARK 465 ILE A 281
REMARK 465 VAL A 282
REMARK 465 GLY A 283
REMARK 465 LYS A 284
REMARK 465 THR A 285
REMARK 465 ALA A 286
REMARK 465 GLU A 287
REMARK 465 GLU A 288
REMARK 465 VAL A 289
So residue 127 is missing as you note which should be perfectly fine since
this is the structure of a mutant of the enzyme where residue 127 has been
deleted. I assume that you want to simulate the deletion mutant version of
the enzyme?
Then we have a ton of residues with missing atoms. So a whole chunk of the
end of the peptide chain is missing from the pdb structure. You will likely
have to decide what to do with this - do you just ignore these residues? Or
homology model them in? Or look for a better crystal structure? This is
really a research decision that you will have to make yourself based on your
judgement.
With regards to the bad contacts if you look at residue MET 154 (/155) it
points right out into solvent so I suspect it may be clashing with solvent
molecules. Did you delete the crystal waters? - if not you probably should
delete them. Then if this doesn't work follow Carlos's advice and try
minimizing in gas phase or with GB first and then solvate in leap.
You could also try running 100 steps or so of MD with a very short time
step, say dt=0.0001. Make sure shake is turned off - then set ntwx=1 and run
and you can then watch the system blow up in VMD. This way you should be
able to see visualy where the problem is coming from and hopefully fix it.
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of devrani mitra
> Sent: Tuesday, May 29, 2007 18:13
> To: amber.scripps.edu
> Subject: Re: AMBER: error in running sander
>
> Thanks a lot for your replies. Well, the same error msg appears even
> if I have deleted Mg-ATP from the pdb. As suggested, I looked at my
> initial pdb structure,
>
> ATOM 919 CG1 VAL A 126 15.020 10.602 2.155 1.00
> 40.87 C
> ATOM 920 CG2 VAL A 126 14.615 12.941 2.762 1.00
> 43.82 C
> ATOM 921 N GLY A 128 17.832 10.976 0.712 1.00
> 52.78 N
> ATOM 922 CA GLY A 128 18.873 10.542 -0.212 1.00
> 59.95 C
>
> However, I found that after 126 it is 128, but this sequence has been
> corrected in 'tleap' as:
>
> ATOM 1831 C VAL 126 36.583 33.672 43.611
> ATOM 1832 O VAL 126 37.744 33.723 44.012
> ATOM 1833 N GLY 127 36.305 33.201 42.383
> ATOM 1834 H GLY 127 35.343 33.143 42.082
>
> Is this the problem?
> Surprisingly, the highest energy is seen at
>
> ATOM 2239 3HE MET 154 48.483 34.334 23.516
>
> This residue is MET 155 at the original starting PDB structure.
> And I looked at this position and did not find any overlapped atoms.
> Could you kindly suggest me as how to fix this?
>
> Thanks again.
> Devrani
>
> N.B. Accidentally I pressed the 'send' button before sending this
> mail, please ignore that blank msg.
>
> On 5/29/07, Ross Walker <ross.rosswalker.co.uk> wrote:
> > Dear Devrani,
> >
> > Here is the first point from your output file:
> >
> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> > 1 1.1843E+11 2.4284E+10 5.5481E+12
> HE3 2239
> >
> > BOND = 156.1910 ANGLE = 724.2956 DIHED =
> > 2575.2795
> > VDWAALS = ************* EEL = -129550.8405 HBOND =
> > 0.0000
> > 1-4 VDW = 1223.8779 1-4 EEL = 11866.6783 RESTRAINT =
> > 0.0000
> >
> > The *'s mean that the value was too large to fit in the
> space provided. Thus
> > your VDW energy is huge and the maximum force GMAX is an
> astounding 5.5 x
> > 10^12 KCal/Mol/A. This likely comes about due to problems
> with your starting
> > structure. You likely have two or more atoms sitting on top
> of each other.
> > Note during minimization the atom with the largest force at
> each step is
> > printed. Above it is at HE3 with number 2239. I suggest you
> visualize your
> > starting structure and look at the area around atome 2239.
> Once you have
> > identified the problem you will need to fix your input
> structure and then
> > re-run the minimization.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of
> delivery, may not
> > be read every day, and should not be used for urgent or
> sensitive issues.
> >
> > > -----Original Message-----
> > > From: owner-amber.scripps.edu
> > > [mailto:owner-amber.scripps.edu] On Behalf Of devrani mitra
> > > Sent: Tuesday, May 29, 2007 14:27
> > > To: amber.scripps.edu
> > > Subject: Re: AMBER: error in running sander
> > >
> > > Hello
> > >
> > > I'm attaching the output file for the details. Hope this
> > > simplifies the things.
> > >
> > > Thanks,
> > > Devrani
> > >
> > > On 5/29/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> > > > does your a_min_water.out file have any information in it?
> > > >
> > > > do the test cases pass?
> > > >
> > > > you need to give us much more information if you want help.
> > > >
> > > >
> > > > On 5/29/07, devrani mitra <devranimitra.gmail.com> wrote:
> > > > > Dear AMBER users,
> > > > >
> > > > > While running sander (for removing the bad contacts)
> following the
> > > > > tutorials, I'm getting the following error message:
> > > > >
> > > > > >> sander -O -i a_min.in -p a.parm7 -c a.crd -r a_min.rst -o
> > > > > a_min_water.out -ref a.rst
> > > > >
> > > > > p0_29153: p4_error: interrupt SIGSEGV: 11
> > > > >
> > > > > I'm not getting as which file do I need to correct.
> > > Please suggest.
> > > > >
> > > > > Thanks!
> > > > > Devrani
> > > > >
> > > > > Devrani Mitra, UC Davis
> > > > >
> > > >
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> majordomo.scripps.edu
> > > > >
> > > >
> > > >
> > > >
> > > >
> > >
> >
> >
> >
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Received on Sun Jun 03 2007 - 06:07:10 PDT
