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
========================================
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