<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>
<div> </div>
<div>Suposed for an unkown molecule, how to assign them on rtp file?</div>
<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>
<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 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 href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a 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>-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20120211/a4d6d18e/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20120211/a4d6d18e/attachment-0001.html</a><br>
<br>------------------------------<br><br>Message: 2<br>Date: Fri, 10 Feb 2012 16:22:18 -0800 (PST)<br>From: MPID <<a href="mailto:mpmcgovern@wisc.edu">mpmcgovern@wisc.edu</a>><br>Subject: [gmx-users] g_wham with cylinder geometry<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <<a href="mailto:1328919738939-4385053.post@n6.nabble.com">1328919738939-4385053.post@n6.nabble.com</a>><br>Content-Type: text/plain; charset=us-ascii<br>
<br>Hi everyone. I ran an umbrella sampling simulation of a protein in a<br>membrane. I used pull_geometry=cylinder. I tried to analyze the results with<br>g_wham. I got this error:<br><br> Fatal error:<br>With pull geometry 'cylinder', expected pulling in Z direction only.<br>
However, found dimensions [Y Y Y]<br><br>The manual says that with this geometry the pulling is in the direction of<br>pull_vec. I set pull_vec to 0 0 1. Do I have to redo these simulations with<br>a line that says pull_dim = N N Y? Or does the data still mean what it is<br>
supposed to, but g_wham is just giving trouble and I can use a different<br>wham program?<br><br>Here is the pull part of my mdp file:<br><br>pull = umbrella<br>pull_geometry = cylinder<br>pull_r0 = 2.0<br>
pull_r1 = 1.5<br>pull_vec1 = 0 0 1<br>pull_start = yes<br>pull_group0 = DPPGB<br>pull_group1 = PROT<br>pull_k1 = 500<br>pull_nstxout = 1000<br>
pull_nstfout = 1000<br><br><br>--<br>View this message in context: <a href="http://gromacs-users-forum.5086.n6.nabble.com/g-wham-with-cylinder-geometry-tp4385053p4385053.html" target="_blank">http://gromacs-users-forum.5086.n6.nabble.com/g-wham-with-cylinder-geometry-tp4385053p4385053.html</a><br>
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.<br><br><br>------------------------------<br><span class="HOEnZb"><font color="#888888"><br>--<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
<br>End of gmx-users Digest, Vol 94, Issue 67<br>*****************************************<br></font></span></blockquote></div><br>