# Re: AMBER: error in running sander

From: devrani mitra <devranimitra.gmail.com>
Date: Wed, 30 May 2007 16:34:41 -0700

On 5/29/07, Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Devrani,
>
> This is not the best pdb structure around :-( For starters it is only at 2.5
>
> 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
> > > 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
> > > > > >
> > > > >
> > > > --------------------------------------------------------------
> > > > ---------
> > > > > > The AMBER Mail Reflector
> > > > > > To post, send mail to amber.scripps.edu
> > > > > > To unsubscribe, send "unsubscribe amber" to
> > majordomo.scripps.edu
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> > >
> > --------------------------------------------------------------
> > ---------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber.scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > >
> > --------------------------------------------------------------
> > ---------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jun 03 2007 - 06:07:17 PDT
Custom Search