Dear Dwight McGee and Amber users,
Thanks for the response.
The error does not seem to be of Maxcycle but for RMS and some other
issue in the receptor_nm.out file, which I did not understand.
Please also suggest which change I should make in the input to handel
this problem.
The files are attached for your kind reference.
The *nm.out files show the following error:
-------------------
_MMPBSA_LIgand_nm.out
***************** ***************** *****************
step = 0
F = 0.374349E+02 GRDMAX = 0.195507E+01 GNORM = 0.428118E+00
E-NONB E-ELE E-HBOND E-BOND
-0.65651E+01 0.78323E+01 0.00000E+00 0.14371E+01
E-ANGLE E-DIHED E-NB14 E-EEL14
0.10720E+02 0.30799E+02 0.16629E+02 -0.23418E+02
E-POL E-3BOD
0.00000E+00 0.00000E+00
Root-mean-square gradient of input coords is 0.4281183951692023
This is greater than the requested maximum: 0.01
------------------------
------------------------
_MMPBSA_receptor_nm.out
PARM file has the title:
Total memory required : 290638717 real words
Total memory required : 11052791 integer words
Total memory required : 14203 4-character words
Maximum nonbond pairs 10753202
ASSERTion ' ier == 0 ' failed in nmode.f at line 106.
------------------------------
On 5/9/11, Dwight McGee <dwight.mcgee.gmail.com> wrote:
> Hi,
>
>>>From you results file
> *WARNINGS:
> igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi
> radii (mbondi)
> Not all of your snapshots minimized within tolerable limits for nmode. *
>
>
> It appears the reason you got those particular results pertaining to the
> nmode calculation in your output file is because not all of your snapshots
> were properly minimized. I would suggest increasing your maximum number of
> cycles. Search through your _MMPBSA*nm.out files to determine where this
> error occurred and the message *"Not minimized properly!"* should be printed
> in the file. It could also be a memory issue but first start with increasing
> the max cycles and rerunning the calculation.
> Hope that help..
>
> On Mon, May 9, 2011 at 12:46 AM, vaibhav dixit
> <vaibhavadixit.gmail.com>wrote:
>
>> Dear Amber users,
>> I had done MD for 3ns for a protein ligand complex. Using this mdcrd
>> file I did MM-PBSA/GBSA along with nmode calculation. I have done
>> these calculations using AMBER10 and AMBERTOOLS1.0.
>> The PB/GB calculation went fine but there seems to be a problem with
>> nmode calculation as all the values listed in
>> FINAL_RESULTS_MMPBSA.dat are 1.0000.
>> Is this result sensible? If not what has gone wrong and what changes
>> do I need to make in my input files so that the result becomes more
>> sensible.
>> Thanking you in anticipation.
>>
>> (FINAL_RESULTS_MMPBSA.dat file is attached for your kind reference.)
>> --
>> With regards
>>
>> Vaibhav A. Dixit
>> Ph.D. Scholar
>> Department of Medicinal Chemistry
>> Natl. Inst. Pharm. Edu. & Res. (NIPER)
>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
>> Punjab -160 062 INDIA
>> Phone (Mobile): +919915214408
>> E-mail: vaibhavadixit.gmail.com
>> www.niper.nic.in
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
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>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Mon May 09 2011 - 00:00:02 PDT
