On 12/02/2012 9:22 AM, Tom wrote:
Dear Mark and Gromacs Users,
Can you be more specific in explanation about improper dihedral of
charmm in gromacs?
For opls aa, it is very clear that every item of improper dihedral
angle is described once
on the *rtp file.
I am quite confused about the one in the charmm.
Ihe same angle is sometimes described twice despite of the difference
in the atoms' sequence.
Like I said last time, different sequence of the same four atoms means
an interaction on a different angle. See manual 4.2.11 and figure
referenced there.
Suposed for an unkown molecule, how to assign them on rtp file?
Working by analogy with those of functional groups in existing .rtp
definitions would be a good start. Find a similar moiety, write out the
connectivity and improper definitions and see what is being done.
Can you give some introduction or show somewhere that has the document?
Gromacs menu does not document about this.
What documentation exists is probably in either the original CHARMM27
force field files (download from web) or the papers that described the
development (references in GROMACS manual). OPLS/AA apparently works
differently, for some reason.
Mark
Thanks for advance!
Tom
Message: 1
Date: Sat, 11 Feb 2012 11:15:04 +1100
From: Mark Abraham <[email protected]
<mailto:[email protected]>>
Subject: Re: [gmx-users] improper dihedral angle in charmm and opls aa
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
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On 11/02/2012 9:54 AM, Tom wrote:
> Dear Gromacs Users
> I am confused about definition of improper dihedral angle in
charmm27,
> which is compared to oplsaa.
> Why charmm ff in gromacs give *double* items for the same
dihedral angle.
> e.g. for charmm27 ASN
> CG ND2 CB OD1
> CG CB ND2 OD1
> ND2 CG HD21 HD22
> ND2 CG HD22 HD21
These are not duplicates. Atom ordering is significant. These
*improper*
dihedral angles are enforcing planarity of the amide moiety. This is
done by influencing dihedral angles along intra-atom vectors where
there
is no bond. OPLS/AA is working differently somehow.
Mark
> in opls aa for ASN
> CG CB CA C dih_ASN_chi1_C_C_C_CO
> CA CB CG ND2 dih_ASN_chi2_C_C_CO_N
> Thanks for advance!
> Tom
> PS:
> the detail is as follows
> ------------------------------------------------
> *in charmm27.ff/aminoacids.rtp*
> [ ASN ]
> [ atoms ]
> N NH1 -0.47 0
> HN H 0.31 1
> CA CT1 0.07 2
> HA HB 0.09 3
> CB CT2 -0.18 4
> HB1 HA 0.09 5
> HB2 HA 0.09 6
> CG CC 0.55 7
> OD1 O -0.55 8
> ND2 NH2 -0.62 9
> HD21 H 0.32 10
> HD22 H 0.30 11
> C C 0.51 12
> O O -0.51 13
> [ bonds ]
> CB CA
> CG CB
> ND2 CG
> N HN
> N CA
> C CA
> C +N
> CA HA
> CB HB1
> CB HB2
> ND2 HD21
> ND2 HD22
> C O
> CG OD1
> [ impropers ]
> N -C CA HN
> C CA +N O
> CG ND2 CB OD1
> CG CB ND2 OD1
> ND2 CG HD21 HD22
> ND2 CG HD22 HD21
> [ cmap ]
> -C N CA C +N
> -------------------------------------------
> in*oplsaa.ff/aminoacids.rtp*
> [ ASN ]
> [ atoms ]
> N opls_238 -0.500 0
> H opls_241 0.300 0
> CA opls_224B 0.140 1
> HA opls_140 0.060 1
> CB opls_136 -0.120 2
> HB1 opls_140 0.060 2
> HB2 opls_140 0.060 2
> CG opls_235 0.500 3
> OD1 opls_236 -0.500 3
> ND2 opls_237 -0.760 4
> HD21 opls_240 0.380 4
> HD22 opls_240 0.380 4
> C opls_235 0.500 5
> O opls_236 -0.500 5
> [ bonds ]
> N H
> N CA
> CA HA
> CA CB
> CA C
> CB HB1
> CB HB2
> CB CG
> CG OD1
> CG ND2
> ND2 HD21
> ND2 HD22
> C O
> -C N
> [ dihedrals ] ; override some with residue-specific ones
> N CA CB CG dih_ASN_chi1_N_C_C_C
> CG CB CA C dih_ASN_chi1_C_C_C_CO
> CA CB CG ND2 dih_ASN_chi2_C_C_CO_N
>
>
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