Actually, I am planning to use AMBER forcefield for both phosphotyrosine and for the system too. The parameters are reliable as they have been published (http://www.springerlink.com/content/u527364w03568353/fulltext.pdf) . But I want to know how to add them to the force field. I have checked the following link :- http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, but I want to do it in a rather shorter way. Like what has been done in the protein ligand tutorial. But will that be ok to do. As in my case also I too have a docked complex .
On Wed, Jun 8, 2011 at 10:26 PM, Dallas Warren <[email protected]>wrote: > What forcefield is that for? Sounds like it is more than likely one of > the AMBER ones.**** > > ** ** > > What forcefield are you using for the rest of your system that you are > simulating?**** > > ** ** > > Are they the same? They should be.**** > > ** ** > > If not, are they compatible? A minor number of them are compatible to some > degree, such as with a version change for a given forcefield. However, vast > majority are not and combining those that aren’t compatible them will make a > nice random number generator that you can spend lots of time using and not > get anything out that is publishable.**** > > ** ** > > See http://www.gromacs.org/Documentation/Terminology/Force_Fields#Usageand > the first point at > http://www.gromacs.org/Documentation/How-tos/Parameterization **** > > ** ** > > Catch ya, > > Dr. Dallas Warren**** > > Medicinal Chemistry and Drug Action**** > > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > [email protected]**** > > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. **** > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > 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/Support/Mailing_Lists > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : [email protected]
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