Dear Ambers,
I am trying to do normal mode analysis using NMODE of amber 7. My
workstation is dual xeon 3.06G CPU,2G memory and the OS is redhat 9.0
Here is what I am doing:
step 1. Get a protein's X-Ray Crystal Structure from PDB, take the
first 80 residues, build .PARM and .CRD files using LEAP(total 1267
atoms after adding H atoms), no water box
step 2. Because NR is generally not for a large system(NR works up to
60 residues in my case; for 80 residues, the job was not finished even
after running 3 days), carry out conjugate gradient minimization using
SANDER:
a. DRMS=1.0E-5
b. CUT=9999.
c. NSNB=9999999
d. MAXCYC=40000, NCYC=500
step 3. To avoid RMSD values problem between Newton-Rhapson and normal
mode calcs, according to the answer at AMBER FAQ, I should write out
the nonbonded pairlist during minimization and reading it back in the
beginning of normal mode calculation. But looks like SANDER does not
have this option to write out nonbonded pairlist(am I wrong??). I try
to run a NR minimization(ntrun=4) to get file "PRLIST". If CG does
find a true minimum at step 2, this step should be finished very
quickly. but I am not sure if it works.
step 4. Normal mode analysis using NMODE(ntrun=1)
The problem at step 2 and 3:
A. CG minimization stopped at cycle 10693 as following:
***********************************************************************
NSTEP ENERGY RMS GMAX NAME
NUMBER
10680 -1.9944E+03 2.1050E-05 3.3197E-04 CD
1050
BOND = 49.1119 ANGLE = 192.7673 DIHED =
719.7927
VDWAALS = -539.9797 EEL = -6284.0420 HBOND =
0.0000
1-4 VDW = 245.6998 1-4 EEL = 3622.2692 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME
NUMBER
10690 -1.9944E+03 1.3108E-05 1.4595E-04 CE2
662
BOND = 49.1119 ANGLE = 192.7673 DIHED =
719.7927
VDWAALS = -539.9797 EEL = -6284.0419 HBOND =
0.0000
1-4 VDW = 245.6998 1-4 EEL = 3622.2692 RESTRAINT =
0.0000
.... RESTARTED DUE TO LINMIN FAILURE ...
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME
NUMBER
10693 -1.9944E+03 1.3107E-05 1.4594E-04 CE2
662
BOND = 49.1119 ANGLE = 192.7673 DIHED =
719.7927
VDWAALS = -539.9797 EEL = -6284.0419 HBOND =
0.0000
1-4 VDW = 245.6998 1-4 EEL = 3622.2692 RESTRAINT =
0.0000
***** REPEATED LINMIN FAILURE *****
***********************************************************************
Is this minimization good enough for NMODE(check RMS values???)? I
read the FAQ about "LINMIN failures", but that is not for this case.
B. Assume the result of minimization is good enough, I continue to the
step 3, a NR job to get PRLIST. At the initial circle of this
job, "rms of step length = 0.0511351183", and the job is not finished
yet after one day. does this mean the reult of CG minimization is not
good?
C. At the amber7 manual, about NMODE gereral description(section 12.2,
Page 248), it is mentioned "Use the double precision version for best
convergence" when using SANDER to do CG minimization. Is there another
version for double precision or just change code in somewhere?
Many thanks for any help!!!
Regards
Dr. Xiaohua Hu
Chemistry Department
Univeristy of Memphis
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Received on Wed Apr 28 2004 - 18:53:00 PDT
