[gmx-users] explicit hydrogen-bond

andrea spitaleri spitaleri.andrea at hsr.it
Wed Jan 31 14:01:04 CET 2007

Hi Lars,
thank for your reply. Indeed you are probably right. On this system I cannot perform successfully a 
posre (see my previous post). The reason is, I think, that the EM cannot yield to a good minimized 
structure (the x-ray resolution  is 3.2A very high). My doubt is now about the "restraints". You 
would use them or nor in the posre simulation? The problem is this ASP-ARG HB is very weak (not a 
standard angle and distance) and edit specbond for taking in account it, in my opinion, it would 
mean "cheating".
This reply should also confirm what Tsjerk says about "solution-crystalline structure".
I will try without restraint doing short MDs starting at 0K -> 300 and the run a MD a 300K. The 
other hypothesis is to run also a short MD then a PS and then the full MD.
I will try both. I let you know

Thanks for now



Lars Schaefer wrote:
> Hi andrea,
> since your Hbond breaks rather early it could be that your system is not 
> completely equilibrated, which could impose some strain on the bond. You 
> could put a distance restraint on that Hbond (and others that are 
> supposed to be imortant) and run for a while before your production 
> simulation.
> Lars
> andrea spitaleri wrote:
>> Hi all,
>> I have a question concerning the H-bond. I am running a 
>> protein-peptide simulation in water.
>> My starting structure is a X-ray complex. What I am observing is that 
>> after 200ps an important hydrogen bond between the peptide and the 
>> protein is breaking (ARG -- ASP). Now, since experimental data and 
>> previous MD (using CHARMM as ff) have demonstrated that this hydrogen 
>> bond is very important for the interaction, I am concluding that in my 
>> case I have a problem with my used ffG43a1.
>> I have been reading few papers and I see that CHARMM ff uses an 
>> explicit hydrogen-bond contribution in the calculation. From the 
>> gromacs manual there is not note about it. In order to validate my 
>> assumption, I am thinking either to swap to ffopls or to perform a 
>> small dynamics at low temperature and increase it to 300K to allow a 
>> better equilibrium.
>> Any suggestion are very welcome.
>> Regards
>> thanks
>> andrea
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Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)

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