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
Regards
Andrea
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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
-------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
