[gmx-users] hbonds in DNA and RNA

[brynza]

Here is typical GC pair from my RNA - charges are reasonable as I may
judge: hbond should be detected between N2-H-O2...
    13     NT      1    GUA     N2      6      -0.83    14.0067   ; qtot -1.47
    14      H      1    GUA    H21      6      0.415      1.008   ; qtot -1.055
    15      H      1    GUA    H22      6      0.415      1.008   ; qtot -0.64

  1602      O     67    CYT     O2    778      -0.38    15.9994   ; qtot -66.64

  electrostatic parameters are standard Cut-oFF 1

  
AVG> On Tue, 2003-05-27 at 13:44, brynza wrote:
>> Hi all,
>> The problem we faced dealing with RNA dynamics is quite confusing:
>> after fixing problems with uracil, adding of all necessary hydrogens,
>> etc, the RNAs we "tortured" both in vacuum and solution lost all
>> complementary interactions and secondary structures distorted
>> substantially. When we tracked all manipulations we did, we found that
>> pdb2gmx cannot find donors, acceptors and as a result no hbonds are
>> formed. For proteins everything is ok. Has anyone faced such problem?
>> And what parameters are responsible for hbond formation in gromacs
>> force field?


AVG> h bonds should follow from electrostatic interactions, not by special
AVG> treatment as used to be in amber. Have you check whether the charges are
AVG> reasonable?

>> Thnx in advance for any helpful suggestions.
>> Timofei,
>> MSU, Chem.Dpt.
>> 
>>   
>> 
>> -- 
>>
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AVG> -- 
AVG> Groeten, David.
AVG> ________________________________________________________________________
AVG> Dr. David van der Spoel,        Dept. of Cell & Mol. Biology
AVG> Husargatan 3, Box 596,          75124 Uppsala, Sweden
AVG> phone:  46 18 471 4205          fax: 46 18 511 755
AVG> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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-- 
Best regards,
 brynza                            mailto:brynza at mail.ru