Re: RE: AMBER: problem with gb md

From: emilia wu <emiliawu.dicp.ac.cn>
Date: Fri, 6 May 2005 14:29:33 +0800

Dear Ross ,
         
       Thank for your suggestions. i checked my initial structure in xleap,and the result is that the unit is ok. when i used igb=2 instead of igb=1, everything is fine, so i think the structure is reasonable.



emilia
        

======= 2005-05-06 12:47:40 艇壓栖佚嶄亟祇=======

>Dear Emilia,
>
>> NSTEP ENERGY RMS GMAX
>> NAME NUMBER
>> 1 nan nan 0.0000E+00
>> C34 1
>>
>> BOND = 199.1390 ANGLE = 606.5759 DIHED
>> = 2318.4901
>> VDWAALS = 134604.7930 EEL = -18304.6508 EGB
>> = nan
>> 1-4 VDW = 1344.4585 1-4 EEL = 11078.6900 RESTRAINT
>> = 0.0000
>> ==============================================================
>> ============
>
>Your VDWAALS term is pretty huge which suggests that there is something very
>wrong with your initial structure. I suggest you check it carefully, you
>likely have two atoms sitting on top of each other.
>
>Try using the check command in xleap and see if any atoms are closer than an
>angstrom or so.
>
>All the best
>Ross
>
>/\
>\/
>|\oss Walker
>
>| Department of Molecular Biology TPC15 |
>| The Scripps Research Institute |
>| Tel:- +1 858 784 8889 |
>| EMail:- ross.rosswalker.co.uk |
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>
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= = = = = = = = = = = = = = = = = = = =
                        

        emilia wu
        emiliawu.dicp.ac.cn
          2005-05-06

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Received on Fri May 06 2005 - 07:53:00 PDT
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