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On 12/02/2012 9:22 AM, Tom wrote:
<blockquote
cite="mid:CAARYzz4amp9koz-RYqmNNG9Ra19yf3u8U8kmK2EaTL0RCijWRA@mail.gmail.com"
type="cite">
<div>Dear Mark and Gromacs Users,</div>
<div> </div>
<div>Can you be more specific in explanation about improper
dihedral of charmm in gromacs?</div>
<div>For opls aa, it is very clear that every item of improper
dihedral angle is described once</div>
<div>on the *rtp file.</div>
<div> </div>
<div>I am quite confused about the one in the charmm.</div>
<div>Ihe same angle is sometimes described twice despite of the
difference in the atoms' sequence.</div>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAARYzz4amp9koz-RYqmNNG9Ra19yf3u8U8kmK2EaTL0RCijWRA@mail.gmail.com"
type="cite">
<div> </div>
<div>Suposed for an unkown molecule, how to assign them on rtp
file?</div>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAARYzz4amp9koz-RYqmNNG9Ra19yf3u8U8kmK2EaTL0RCijWRA@mail.gmail.com"
type="cite">
<div> </div>
<div>Can you give some introduction or show somewhere that has the
document?</div>
<div>Gromacs menu does not document about this.</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAARYzz4amp9koz-RYqmNNG9Ra19yf3u8U8kmK2EaTL0RCijWRA@mail.gmail.com"
type="cite">
<div> </div>
<div>Thanks for advance!</div>
<div> </div>
<div>Tom <br>
</div>
<div class="gmail_quote">
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px
0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><br>
Message: 1<br>
Date: Sat, 11 Feb 2012 11:15:04 +1100<br>
From: Mark Abraham <<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] improper dihedral angle in charmm and
opls aa<br>
To: Discussion list for GROMACS users <<a
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a moz-do-not-send="true"
href="mailto:4F35B308.3080504@anu.edu.au">4F35B308.3080504@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 11/02/2012 9:54 AM, Tom wrote:<br>
> Dear Gromacs Users<br>
> I am confused about definition of improper dihedral angle
in charmm27,<br>
> which is compared to oplsaa.<br>
> Why charmm ff in gromacs give *double* items for the same
dihedral angle.<br>
> e.g. for charmm27 ASN<br>
> CG ND2 CB OD1<br>
> CG CB ND2 OD1<br>
> ND2 CG HD21 HD22<br>
> ND2 CG HD22 HD21<br>
<br>
These are not duplicates. Atom ordering is significant. These
*improper*<br>
dihedral angles are enforcing planarity of the amide moiety.
This is<br>
done by influencing dihedral angles along intra-atom vectors
where there<br>
is no bond. OPLS/AA is working differently somehow.<br>
<br>
Mark<br>
<br>
> in opls aa for ASN<br>
> CG CB CA C dih_ASN_chi1_C_C_C_CO<br>
> CA CB CG ND2 dih_ASN_chi2_C_C_CO_N<br>
> Thanks for advance!<br>
> Tom<br>
> PS:<br>
> the detail is as follows<br>
> ------------------------------------------------<br>
> *in charmm27.ff/aminoacids.rtp*<br>
> [ ASN ]<br>
> [ atoms ]<br>
> N NH1 -0.47 0<br>
> HN H 0.31 1<br>
> CA CT1 0.07 2<br>
> HA HB 0.09 3<br>
> CB CT2 -0.18 4<br>
> HB1 HA 0.09 5<br>
> HB2 HA 0.09 6<br>
> CG CC 0.55 7<br>
> OD1 O -0.55 8<br>
> ND2 NH2 -0.62 9<br>
> HD21 H 0.32 10<br>
> HD22 H 0.30 11<br>
> C C 0.51 12<br>
> O O -0.51 13<br>
> [ bonds ]<br>
> CB CA<br>
> CG CB<br>
> ND2 CG<br>
> N HN<br>
> N CA<br>
> C CA<br>
> C +N<br>
> CA HA<br>
> CB HB1<br>
> CB HB2<br>
> ND2 HD21<br>
> ND2 HD22<br>
> C O<br>
> CG OD1<br>
> [ impropers ]<br>
> N -C CA HN<br>
> C CA +N O<br>
> CG ND2 CB OD1<br>
> CG CB ND2 OD1<br>
> ND2 CG HD21 HD22<br>
> ND2 CG HD22 HD21<br>
> [ cmap ]<br>
> -C N CA C +N<br>
> -------------------------------------------<br>
> in*oplsaa.ff/aminoacids.rtp*<br>
> [ ASN ]<br>
> [ atoms ]<br>
> N opls_238 -0.500 0<br>
> H opls_241 0.300 0<br>
> CA opls_224B 0.140 1<br>
> HA opls_140 0.060 1<br>
> CB opls_136 -0.120 2<br>
> HB1 opls_140 0.060 2<br>
> HB2 opls_140 0.060 2<br>
> CG opls_235 0.500 3<br>
> OD1 opls_236 -0.500 3<br>
> ND2 opls_237 -0.760 4<br>
> HD21 opls_240 0.380 4<br>
> HD22 opls_240 0.380 4<br>
> C opls_235 0.500 5<br>
> O opls_236 -0.500 5<br>
> [ bonds ]<br>
> N H<br>
> N CA<br>
> CA HA<br>
> CA CB<br>
> CA C<br>
> CB HB1<br>
> CB HB2<br>
> CB CG<br>
> CG OD1<br>
> CG ND2<br>
> ND2 HD21<br>
> ND2 HD22<br>
> C O<br>
> -C N<br>
> [ dihedrals ] ; override some with residue-specific ones<br>
> N CA CB CG dih_ASN_chi1_N_C_C_C<br>
> CG CB CA C dih_ASN_chi1_C_C_C_CO<br>
> CA CB CG ND2 dih_ASN_chi2_C_C_CO_N<br>
><br>
><br>
<br>
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