Thanks for your kind reply. Maybe I made a mistake unintentionally in modification of files. The CT2 in charmm folder I downloaded from the source, is the same as you wrote. Thanks.
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <[email protected]> To: Discussion list for GROMACS users <[email protected]> Cc: Sent: Thursday, January 3, 2013 2:47 PM Subject: Re: Fw: [gmx-users] Amidated C-terminal On 1/3/13 6:11 AM, Shima Arasteh wrote: > Have a look at CT2 in aminoacids.c.tdb please: > > [ CT2 ] > [ replace ] > O CC 12.011 0.55 > O O 15.9994 -0.55 > > > It is +0.55 as what you said. But I see all carbonyl C in aminoacids.rtp file > have +0.51 charge. > I think the amidated C-terminal in my top file should be charged +0.55 as > what I see in c.tdb. Shouldn't be? Why it couldn't understand to take +0.55 > charge for this last residue? > There is an error in the .tdb file. The first [replace] line attempts to replace an O atom and assign it a CC type with charge of +0.55, which is then overridden by the next line, which assigns the O atom an O type with -0.55 charge. The carbonyl C is (erroneously) not adjusted. The correct line is present in the charmm27.ff folder: [ CT2 ] [ replace ] C CC 12.011 0.55 O O 15.9994 -0.55 -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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 -- 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
