[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
Justin Lemkul
jalemkul at vt.edu
Wed Dec 12 18:12:17 CET 2012
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 <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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>>
--
========================================
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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