On 12/15/12 1:34 PM, James Starlight wrote:
The last problem with which I've forced during preparation of my
chromophore is when I've defined bond between chromophore and the next
residue
C +N
That produce 15 addition errors about unknown UB and dihedral types
in the atoms of the next residue (not in the chromophore) where all UB
and impropers must be defined initially.
Why that occurs ?
Because the combinations of parameters don't exist in ffbonded.itp.
-Justin
2012/12/14, James Starlight <jmsstarli...@gmail.com>:
The topology with the below params produced that 118 errors during
grompp processings ( after pdb2gmx processing the geoetry of the
mollecule was correct )
[CRN]
[ atoms ]
CG2 CA -0.0900 0
CD1 CA -0.0800 1
CD2 CA -0.0800 2
CE1 CA -0.2800 3
CE2 CA -0.2800 4
CZ CA 0.4500 5
N NH1 -0.4700 6
CA1 CPH1 0.1000 7
CB1 CT1 -0.1400 8
CG1 CT3 0.0900 9
OG1 OH1 -0.6600 10 ;!-0.6800
C1 CPH2 0.5000 11
N2 NR2 -0.6000 12
N3 NR1 -0.5700 13
C2 CPH1 0.5700 14
O3 O -0.5700 15
CA2 CPH1 0.1000 16
CA3 CPH1 0.1000 17
C C 0.5100 18
O O -0.5100 19
CB2 CE1 -0.1400 20
OH O -0.6200 21
HA1 HB 0.0700 22
HA32 HB 0.0700 23
HA33 HB 0.0700 24
HD1 HP 0.1400 25
HD2 HP 0.1400 26
HE1 HP 0.1000 27
HE2 HP 0.1000 28
HG11 HA 0.0900 29
HG12 HA 0.0900 30
HG13 HA 0.0900 31
HOG1 H 0.4300 32
HB2 HA1 0.2100 33
H11 H 0.3700 34
HB1 HA1 0.2100 36
[ bonds ]
HG11 CG1
HG12 CG1
CG1 HG13
CG1 CB1
OG1 HOG1
OG1 CB1
CB1 HB1
CB1 CA1
HE2 CE2
N H11
N CA1
CA1 HA1
CA1 C1
CE2 CD2
CE2 CZ
HD2 CD2
OH CZ
CD2 CG2
CZ CE1
N2 C1
N2 CA2
C1 N3
HA33 CA3
CG2 CB2
CG2 CD1
CE1 HE1
CE1 CD1
CA2 CB2
CA2 C2
N3 CA3
N3 C2
CB2 HB2
CA3 C
CA3 HA32
CD1 HD1
C2 O3
C O
[ impropers ]
CG2 CD1 CB2 CD2
CD1 CE1 CG2 HD1
CD2 CE2 CG2 HD2
CE2 CZ CD2 HE2
CB2 CA2 CG2 HB2
CA2 N2 CB2 C2
C1 CA1 N2 N3
CA1 N C1 CB1
CA1 CB1 C1 HA1
CB1 OG1 CA1 CG1
CB1 CG1 CA1 HB1
C2 N3 CA2 O3
N3 C2 C1 CA3
CA3 C N3 HA33
CA3 HA33 N3 HA32
CZ CE1 CE2 OH
CE1 CZ CD1 HE1
CG1 HG11 CB1 HG12
CG1 HG11 CB1 HG13
; with next residue
C +N CA3 O
; with previous residue
N -C CA1 H11
[ cmap ]
-C N CA1 C1 N2
CA2 C2 N3 CA3 C
The only in that I not sure in that model is the corrections in the
cmap.itp which I added (I've used first two terms which are correspond
to the backbone atoms of the standart amino acid:
C NH1 CT1 C NH1 1 24 24\
C NH1 CT1 C N 1 24 24\
and renamed it to the chromophore atom names)
by the way If you had had your rtp of the chromophore which you've
done in accordance to that paper could you provide me with them for
comparison with my model ?
James
2012/12/14, Justin Lemkul <jalem...@vt.edu>:
On 12/14/12 3:20 PM, James Starlight wrote:
Justin,
in the case of the system with the atom types assigned from that paper
the grompp produced above 118 errors of non standard bond, angle as
well as dihedral types ;o So it' seems that some 118 addition terms
must be added to the ffbonded.itp to the existing charmm parameters(
it's uncommon for me because in that case the atom names werefrom
standart charmm ff but the total number of errors was bigger than in
case of Swiss params non-standart names usage).
I'm not sure why there were so many errors when you used those
parameters.
Like
I said, we've used them before. I recall a few errors along the way, but
manual
assignment of the bonded parameters according to the paper is fairly
straightforward.
By the way I've simulated choromophore produced by SWISS ( with the
charges assigned from the paper) in the vacuum and didnt notice any
inaccuracy in the conformation of chromophore. So the last that I
should is the carefull assignment of the 9 missed dihedral terms with
the rest of the protein.
Sounds like a reasonably approach. Good luck.
-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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========================================
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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