[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
James Starlight
jmsstarlight at gmail.com
Wed Dec 12 17:49:01 CET 2012
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)
[ 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 ]
-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 <jmsstarlight at gmail.com>:
> 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 <jalemkul at vt.edu>:
>>
>>
>> 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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