Dear Itamar Thank you for the reply.
If I modify Cys parameters in the *rtp file in order to add the Cys-label parameters, it will be applied to other Cys in the protein as well. Isn't it? In case of modification of *itp file, should I modify all nr or qtot after the Cys? What about bonds? Best, Faezeh On Thu, Jul 21, 2011 at 5:51 AM, Itamar Kass <[email protected]> wrote: > Hi Faezeh, > > You can modify the FF and add the Cys-label parameters to the *rtp and *hdb > files, such that pdb2gmx will be able to use them. Another why is use the > original pdb as a starting point and modify the output *gto, *itp and *top > files. > > Just remember that in anycase, it is better to copy the files into your > local directory so an change you made will not effect other simulations. > > Cheers, > Itamar > > > PS I can recommend on this site which can help you in the process > http://compbio.biosci.uq.edu.au/atb/ > > > On 21/07/11 7:43 PM, Faezeh Nami wrote: > > Dear all > > I am trying to simulate a protein which a label (a small organic > molecule) is covalently attached to a cysteine. Worth to say there is no > label in the original pdb file of protein and it was attached to the Cys. > using a software. > Should I insert the label parameters into the conf.gro file or I need to > modify a force field? If there is someone who has experiences in such > systems, please have some advice. > > Thanks in advance, > Faezeh > > > > > > -- > > > "In theory, there is no difference between theory and practice. But, in > practice, there is." - Jan L.A. van de Snepscheut > > =========================================== > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: [email protected] > ============================================ > > > -- > 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 >
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