Dear Dr Ross,
As per your sugesstions, I tried to inspect the whole structure visually but
I didn't find anything unusual. Then I tried to minimise separately both
protein and the ligand, which completed successfully. So in my opinion, the
problem only comes when both protein and ligand are present as a complex.
Since the ligand is interacting with the protein through non bonded
interaction, this might be causing some problem. I thought you might be have
some idea on this aspect.
Is there any way to add the ligand to the protein through xleap?
-John
On 12/10/08, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> Hi John,
>
>
>
> I assume all of the test cases passed in serial and parallel.
>
>
>
> If you look closely at your calculation output you will see that the angle
> term is infinite and your vdwaals term is very high. This suggests that you
> have a very strained initial structure. It is strange for the angle term to
> be infinite (or very large), normally it is bond terms that end up very high
> or the EEL/VDW terms.
>
>
>
> I would suggest visually looking at your starting structure to see if you
> can see what is wrong with - I would focus on atom HE1 (4173) which has the
> highest force on it.
>
>
>
> All the best
>
> Ross
>
>
>
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *john smith
> *Sent:* Tuesday, December 09, 2008 10:21 PM
> *To:* amber
> *Subject:* AMBER: forrtl severe(174) error with minimization and md
>
>
>
> Dear all,
>
>
> I have compile the AMBER10 and AmberTools1.0 on IBM PC with Intel Pentium 4
> processor using RedHat EL4 linux, AMBER was compiled with inter fortran
> compiler. All the test have passed during the installation.
> And I am trying to run molecular dynamics of ligand docked into the
> protein. I have prepared the *.top and *.crd files. However, whaen I run the
> sander it stops abruptly with the following error (for minimisation &
> molecular dynamics both ).
>
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>
> Image PC Routine Line Source
>
> libc.so.6 00489410 Unknown Unknown Unknown
>
> libc.so.6 0048AF81 Unknown Unknown Unknown
>
> sander 08754169 Unknown Unknown Unknown
>
> sander 0872C08D Unknown Unknown Unknown
>
> sander 0872F1A7 Unknown Unknown Unknown
>
> libpthread.so.0 0011C7C0 Unknown Unknown Unknown
>
> sander 083B2A92 Unknown Unknown Unknown
>
> sander 0812B671 Unknown Unknown Unknown
>
> sander 081192ED Unknown Unknown Unknown
>
> sander 08115C95 Unknown Unknown Unknown
>
> sander 0804B1F5 Unknown Unknown Unknown
>
> libc.so.6 0043BE23 Unknown Unknown Unknown
>
> sander 0804B131 Unknown Unknown Unknown
>
> My input file is
>
> m8-minisation
>
> &cntrl
>
> imin=1, maxcyc =500,
>
> ncyc = 250, ntb = 0, ntpr =1,
>
> igb = 0, cut = 12,
>
> /
>
>
> The output file shows following lines
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
>
> 1 NaN NaN 7.0438E+08 HE1 4173
>
> BOND = 512.6780 ANGLE = NaN DIHED = 3135.6235
>
> VDWAALS = 70560903.2313 EEL = -20856.2773 HBOND = 0.0000
>
> 1-4 VDW = 2043.2988 1-4 EEL = 14310.2031 RESTRAINT = 0.0000
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
>
> 2 NaN NaN 0.0000E+00 N 1
>
> BOND = NaN ANGLE = NaN DIHED = NaN
>
> VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
>
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
>
>
> I had tried different value of cutoff and ntpr, but all gave the same
> result. I cannot understand what the problem is. Please suggest me some
> solution to this problem
>
> thanks in advance
>
> -John
>
>
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Received on Mon Dec 15 2008 - 01:14:23 PST
