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? Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <[email protected]> To: Shima Arasteh <[email protected]>; Discussion list for GROMACS users <[email protected]> Cc: Sent: Thursday, January 3, 2013 2:24 PM Subject: Re: Fw: [gmx-users] Amidated C-terminal On 1/3/13 1:00 AM, Shima Arasteh wrote: > > > > > > > The version of GROMACS I'm using is 4.5.5. > I checked the aminiacids.rtp file in charmm36 folder, I see + 0.51 for > carbonyl C. Is there any problem with the C36 which I use? > Probably. Check the aminoacids.c.tdb file as well, it may not be correct. I used the standard charmm27.ff for my test and it worked fine. -Justin > [ SER ] > [ atoms ] > N NH1 -0.47 0 > HN H 0.31 1 > CA CT1 0.07 2 > HA HB 0.09 3 > CB CT2 0.05 4 > HB1 HA 0.09 5 > HB2 HA 0.09 6 > OG OH1 -0.66 7 > HG1 H 0.43 8 > C C 0.51 9 > O O -0.51 10 > > > > > Sincerely, > Shima > > > ________________________________ > From: Justin Lemkul <[email protected]> > To: Shima Arasteh <[email protected]>; Discussion list for GROMACS > users <[email protected]> > Sent: Wednesday, January 2, 2013 10:46 PM > Subject: Re: [gmx-users] Amidated C-terminal > > > > On 1/2/13 2:07 PM, Shima Arasteh wrote: >> >> >> Hi, >> >> In order to make an amidated c-terminal, I used CT2 in charmm ff at the >> c-terminal. The last residue of my peptide is serine, and the total charge >> of peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at >> the c-terminal, and then getting top file, when I see the top file, >> everything is ok up to the amidated serine residue. But something wrong is >> with the charged amidated serine; the total charge is not equal to 5.00 : >> >> . >> . >> . >> 361 C 22 LYS C 361 0.51 12.011 ; >>qtot 5.51 >> 362 O 22 LYS O 362 -0.51 15.999 ; >>qtot 5 >> ; residue 23 SER rtp SER q -0.0 >> 363 NH1 23 SER N 363 -0.47 14.007 ; >>qtot 4.53 >> 364 H 23 SER HN 364 0.31 1.008 ; >>qtot 4.84 >> 365 CT1 23 SER CA 365 0.07 12.011 ; >>qtot 4.91 >> 366 HB 23 SER HA 366 0.09 1.008 ; >>qtot 5 >> 367 CT2 23 SER CB 367 0.05 12.011 ; >>qtot 5.05 >> 368 HA 23 SER HB1 368 0.09 1.008 ; >>qtot 5.14 >> 369 HA 23 SER HB2 369 0.09 1.008 ; >>qtot 5.23 >> 370 OH1 23 SER OG 370 -0.66 15.999 ; >>qtot 4.57 >> 371 H 23 SER HG1 371 0.43 1.008 ; >>qtot 5 >> 372 C 23 SER C 372 0.51 12.011 ; >>qtot 5.51 >> 373 NH2 23 SER NT 373 -0.62 14.007 ; >>qtot 4.89 >> 374 H 23 SER HT1 374 0.3 1.008 ; >>qtot 5.19 >> 375 H 23 SER HT2 375 0.32 1.008 ; >>qtot 5.51 >> 376 O 23 SER O 376 -0.55 15.999 ; >>qtot 4.96 >> >> I'm wondering if it is incorrect to use CT2 as the c-terminal? Why the last >> residue is positive charged? Do the defined atom charges are supposed to be >> modified in last residue ? >> > > The choice of CT2 is correct. The net charge comes from an incorrect charge > assignment to the carbonyl C (atom 372), which should be +0.55 instead of > +0.51, > which is the charge in a normal backbone peptide bond. The aminoacids.c.tdb > file correctly assigns this charge, so I don't know why pdb2gmx didn't produce > it. I tried a protein in version 4.5.5 and it worked perfectly - which > version > are you using? If it's not 4.5.5, upgrade and try again. > > -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
