On 12/12/12 11:49 AM, James Starlight wrote:
New problem during processing of y structure via GROMPP
ERROR 217 [file topol.top, line 34183]:
No default Improper Dih. types
ERROR 218 [file topol.top, line 34184]:
No default Improper Dih. types
ERROR 219 [file topol.top, line 34185]:
No default Improper Dih. types
ERROR 220 [file topol.top, line 34186]:
No default Improper Dih. types
ERROR 221 [file topol.top, line 34187]:
No default Improper Dih. types
-------------------------------------------------------
Fatal error:
Unknown cmap torsion between atoms 915 917 919 934 946
1) Does the errors about Improper types due to non-standart atom names
in the RTP? Must I use only standard charmm atom names in that section
? ( I've used Swiss Param's abbreviation see below)
The names are irrelevant, but the types are what lead to the error. The CMAP
torsions should only involve backbone atoms, and therefore no special types are
needed. You should be using standard CHARMM atom types.
[ 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
2 ) In the fatal error the 915 917 919 93 atoms is the C atom of i-2
N Cb C atoms of i-1 and N of the i-residue where i is the
chromophore.
In the RTP file I notice that CMAP for standard amino acids is the
from N to C end of the corresponded and\or adjacent residues. How I
could define it for my chromophore composed from 3 residues-like
objects ? Should something like below example work ? Also I didnt
observe such CMAP for HEME molecule.
CMAP is only applied to backbone atoms. It should be possible to define the
chromophore's backbone just like any other residue. Heme will not have any CMAP
terms because it is a prosthetic group and does not have any backbone atoms.
-Justin
[ cmap ]
-C N CA1 C1 N3
C1 N3 CA3 C +N
In tht exmple -C and +N atoms of adjacent residues and others atoms
are from chromophore.
James
2012/12/12, James Starlight <[email protected]>:
Justin,
The IMPROPERS consisted of atom names (its correct as I understood).
The bond tern I've changed. The resulted RTP
[CRO]
[ atoms ]
CG2 CB 0.0284 0
CD1 CB -0.1500 1
CD2 CB -0.1500 2
CE1 CB -0.1500 3
CE2 CB -0.1500 4
CZ CB 0.0825 5
N NC=O -0.7301 6
CA1 CR 0.3611 7
CB1 CR 0.2800 8
CG1 CR 0.0000 9
OG1 OR -0.6800 10
C1 C=O 0.4490 11
N2 N=C -0.6210 12
N3 NC=O -0.4201 13
C2 C=O 0.6156 14
O3 O=C -0.5700 15
CA2 C=C 0.1854 16
CA3 CR 0.3611 17
C C=O 0.5690 18
O O=C -0.5700 19
CB2 C=C -0.1784 20
OH OR -0.5325 21
HA1 HCMM 0.0000 22
HA32 HCMM 0.0000 23
HA33 HCMM 0.0000 24
HD1 HCMM 0.1500 25
HD2 HCMM 0.1500 26
HE1 HCMM 0.1500 27
HE2 HCMM 0.1500 28
HG11 HCMM 0.0000 29
HG12 HCMM 0.0000 30
HG13 HCMM 0.0000 31
HOG1 HOR 0.4000 32
HB2 HCMM 0.1500 33
H11 HNCO 0.3700 34
HH HOCC 0.4500 35
HB1 HCMM 0.0000 36
[ bonds ]
HG11 CG1
HG12 CG1
CG1 HG13
CG1 CB1
OG1 HOG1
OG1 CB1
CB1 HB1
CB1 CA1
HE2 CE2
N H11
N CA1
HH OH
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
That produce correct structure from my eGFP model :) But I suppose
that charges should be changed in accordance to the paper which you
provide me ( in my case charges were assigned by Swiss Param's
building blocks)
Thanks for help
James
2012/12/12, Justin Lemkul <[email protected]>:
On 12/12/12 6:54 AM, James Starlight wrote:
Oh that problem was imperically resolved by renamind O2 ( which are
not terminal but pdb2gmx define them as a terminal ) atom to O3
The only question about my chromophore is the definition of the IMPROPER
groups.
As I've posted above my initial model was CAPPED from C and N termi by
NH2 and Ace. The resulted topology consisted of Improper for bonds
between chromophore atoms and Capped groups ( e.g :
With ACE (C-3 O-1 C-4 H-11 H-12 H-1 )
IMPH C N1 CA3 O
IMPH N C3 CA1 H11
IMPH C3 O1 N C4
IMPH C4 HC11 C3 H1
IMPH C4 HC11 C3 H12
With NH2 (N1-H2-H3)
IMPH N1 H2 C H3
IMPH C N1 CA3 O
That strings were removed from chromophore RTP. But in my final model
there are 2 amino acids insted of capped groups so the IPROPERS must
be inclusion for protein-chromophore nonds. How it could be done ?
In some amino acids I've found -N and -C blocks that (if I understood
correctly) for C and N atoms of the adjacent residues. How that atoms
must be defined correctly in the protein-chromophore comples ?
+ and - indicate next and previous residues, respectively. Presumably
your
chromophore engages in the same types of peptide bonds as any other amino
acid,
so the syntax is the same as any other case.
-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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