<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br><div><div>3 mar 2011 kl. 10.17 skrev <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">but I have the torsion angles , bond angles for my residue .. The problem<br>is I don't know which one to put where as the charmm FF parameter that I<br>have got doesnot match with the charmm ff parameter in gromacs.. that's y I<br>am confused ..</span></blockquote></div><br></div><div>I don't fully understand but the parameters you listed are from CHARMM so to convert them to GROMACS you have to compare the functional forms (they are listed in the header for each type) with the GROMACS ones and also convert the units. </div><div><br></div><div><blockquote type="cite"></blockquote></div><blockquote type="cite"><div><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I followed the tutorial -<br></blockquote><blockquote type="cite"><a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a> for<br></blockquote><blockquote type="cite">updating the Charmm FF for my modified residue ..<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I added the residues to the .rtp file , then I added the new atom types in<br></blockquote><blockquote type="cite">.atp file ,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The compound has some linkage with serine and glycine ... I want to know<br></blockquote><blockquote type="cite">how and where shall I add the linkage parameters and the parameters (in<br></blockquote><blockquote type="cite">bits) given below<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">(The parameter file of the compound looks like this ) ..<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">BONDS<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!V(bond) = Kb(b - b0)**2<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!Kb: kcal/mole/A**2<br></blockquote><blockquote type="cite">!b0: A<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!atom type Kb b0<br></blockquote><blockquote type="cite">CA1 CA2 305.00 1.3750 !<br></blockquote><blockquote type="cite">CA2 CA3 305.00 1.3750 !<br></blockquote><blockquote type="cite">CA3 CA4 305.00 1.3750 !<br></blockquote><blockquote type="cite">HPc CA1 340.000 1.08 !<br></blockquote><blockquote type="cite">HPc CA2 340.000 1.08 !<br></blockquote><blockquote type="cite">HPc CA3 340.000 1.08 !<br></blockquote><blockquote type="cite">HPc CA4 340.000 1.08 !<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">ANGLES<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!V(angle) = Ktheta(Theta - Theta0)**2<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!V(Urey-Bradley) = Kub(S - S0)**2<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!Ktheta: kcal/mole/rad**2<br></blockquote><blockquote type="cite">!Theta0: degrees<br></blockquote><blockquote type="cite">!Kub: kcal/mole/A**2 (Urey-Bradley)<br></blockquote><blockquote type="cite">!S0: A<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!atom types Ktheta Theta0 Kub S0<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">NR2c CP2c NR1c 130.00 114.00 !<br></blockquote><blockquote type="cite">CP2c NR2c CP1c 130.00 106.00 !<br></blockquote><blockquote type="cite">CP2c NR1c CP1c 130.00 107.90 !<br></blockquote><blockquote type="cite">NR2c CP1c CP1c 130.00 108.30 !<br></blockquote><blockquote type="cite">NR2c CP1c CE1c 45.80 129.50 !<br></blockquote><blockquote type="cite">NR1c CP1c OcH 42.00 126.00 !<br></blockquote><blockquote type="cite">NR1c CP1c CP1c 130.00 103.00 !<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">!Connection to the ser fragment<br></blockquote><blockquote type="cite">!------------------------------<br></blockquote><blockquote type="cite">CT2 CT1 CP2c 52.000 108.0000 ! ALLOW ALI PEP POL ARO<br></blockquote><blockquote type="cite">HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP<br></blockquote><blockquote type="cite">NH1 CT1 CP2c 50.000 107.0000 ! ALLOW PEP POL ARO ALI<br></blockquote><blockquote type="cite">NR2C CP2C CT1 40.00 125.00 !<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">!Connection to the gly fragment<br></blockquote><blockquote type="cite">!------------------------------<br></blockquote><blockquote type="cite">NR1C CT2 C 50.000 107.0000<br></blockquote><blockquote type="cite">NR1c CT2 HB 48.000 108.0000<br></blockquote><blockquote type="cite">CP2C NR1C CT2 36.00 129.00<br></blockquote><blockquote type="cite">CP1C NR1C CT2 32.00 123.40<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">DIHEDRALS<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!V(dihedral) = Kchi(1 + cos(n(chi) - delta))<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!Kchi: kcal/mole<br></blockquote><blockquote type="cite">!n: multiplicity<br></blockquote><blockquote type="cite">!delta: degrees<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!atom types Kchi n delta<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">CP2C NR2C CP1C CP1C 14.0000 2 180.00 !<br></blockquote><blockquote type="cite">CP2C NR1C CP1C CP1C 14.0000 2 180.00 !<br></blockquote><blockquote type="cite">NR2C CP2C NR1C CP1C 14.0000 2 180.00 !<br></blockquote><blockquote type="cite">NR2C CP1C CP1C NR1C 4.0000 2 180.00 !<br></blockquote><blockquote type="cite">NR1C CP2C NR2C CP1C 4.0000 2 180.00 !<br></blockquote><blockquote type="cite">CA1 CA2 CA3 CA4 3.1000 2 180.00 !<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">!barrier CA-CB<br></blockquote><blockquote type="cite">CP1C CP1C CE1C HA1C 6.84 2 180.00 !<br></blockquote><blockquote type="cite">CP1C CP1C CE1C CA1 6.84 2 180.00 !<br></blockquote><blockquote type="cite">NR2C CP1C CE1C HA1C 6.84 2 180.00 !<br></blockquote><blockquote type="cite">NR2C CP1C CE1C CA1 6.84 2 180.00 !<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!barrier CB-CG2<br></blockquote><blockquote type="cite">CP1C CE1C CA1 CA2 1.4 2 180.00 !<br></blockquote><blockquote type="cite">HA1C CE1C CA1 CA2 1.4 2 180.00 !<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">CP2C NR1C CP1C OCH 14.00 2 180.00 !<br></blockquote><blockquote type="cite">NR2C CP2C NR1C CT2 14.00 2 180.00 !<br></blockquote><blockquote type="cite">NR2C CP1C CP1C OCH 14.00 2 180.00 !<br></blockquote><blockquote type="cite">CP1C NR1C CP2C CT1 14.00 2 180.00 !<br></blockquote><blockquote type="cite">OCH CP1C NR1C CT2 14.00 2 180.00 !<br></blockquote><blockquote type="cite">CP1C NR2C CP2C CT1 14.00 2 180.00 !<br></blockquote><blockquote type="cite">CP1C CP1C NR1C CT2 14.00 2 180.00 !<br></blockquote><blockquote type="cite">CT1 CP2C NR1C CT2 14.00 2 180.00 !<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">! Linking the chromophore and the glycine fragment<br></blockquote><blockquote type="cite">O C CT2 NR1C 0.0000 1 0.00 !<br></blockquote><blockquote type="cite">NH1 C CT2 NR1c 0.6000 1 0.00 !<br></blockquote><blockquote type="cite">CP2C NR1C CT2 HB 0.032 3 0.00 !<br></blockquote><blockquote type="cite">CP2c NR1c CT2 C 0.032 3 0.00 !<br></blockquote><blockquote type="cite">CP1c NR1c CT2 HB 0.032 3 180.00 !<br></blockquote><blockquote type="cite">CP1c NR1c CT2 C 0.032 3 180.00 !<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">! Linking the chromophore and the serine fragment<br></blockquote><blockquote type="cite">C NH1 CT1 CP2C 0.2000 1 180.00 !<br></blockquote><blockquote type="cite">H NH1 CT1 CP2C 0.0000 1 0.00 !<br></blockquote><blockquote type="cite">NR2C CP2C CT1 HB 0.105 3 180.00 !<br></blockquote><blockquote type="cite">NR2C CP2C CT1 NH1 0.105 3 180.00 !<br></blockquote><blockquote type="cite">NR2C CP2C CT1 CT2 0.105 3 180.00 !<br></blockquote><blockquote type="cite">NR1C CP2C CT1 HB 0.105 3 0.00 !<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">IMPROPER<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!V(improper) = Kpsi(psi - psi0)**2<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!Kpsi: kcal/mole/rad**2<br></blockquote><blockquote type="cite">!psi0: degrees<br></blockquote><blockquote type="cite">!note that the second column of numbers (0) is ignored<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!atom types Kpsi psi0<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">CP2C NR2C NR1C CT1 0.5 0 0.00<br></blockquote><blockquote type="cite">CP2C NR1C NR2C CT1 0.5 0 0.00<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">CP1C NR1C CP1C OCH 0.5 0 0.00<br></blockquote><blockquote type="cite">CP1C CP1C NR1C OCH 0.5 0 0.00<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">NR1C CP1C CP2C CT2 0.45 0 0.00<br></blockquote><blockquote type="cite">NR1C CP2C CP1C CT2 0.45 0 0.00<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">CP1C NR2C CP1C CE1C 220.0 0 0.00<br></blockquote><blockquote type="cite">CP1C CP1C NR2C CE1C 220.0 0 0.00<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)<br></blockquote><blockquote type="cite">!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!CAc 5.000000 -0.070000 1.992400 ! ALLOW ARO<br></blockquote><blockquote type="cite">! ! benzene (JES)<br></blockquote><blockquote type="cite">CA1 5.000000 -0.070000 1.992400 ! ALLOW ARO<br></blockquote><blockquote type="cite">CA2 5.000000 -0.070000 1.992400 ! ALLOW ARO<br></blockquote><blockquote type="cite">CA3 5.000000 -0.070000 1.992400 ! ALLOW ARO<br></blockquote><blockquote type="cite">CA4 5.000000 -0.070000 1.992400 ! ALLOW ARO<br></blockquote><blockquote type="cite">CE1c 0.000000 -0.068000 2.090000 !<br></blockquote><blockquote type="cite">! for propene, yin/adm jr., 12/95<br></blockquote><blockquote type="cite">CP1c 0.000000 -0.050000 1.800000 ! ALLOW ARO<br></blockquote><blockquote type="cite"> ! adm jr., 10/23/91, imidazole solvation and sublimation<br></blockquote><blockquote type="cite">CP2c 0.000000 -0.050000 1.800000 ! ALLOW ARO<br></blockquote><blockquote type="cite"> ! adm jr., 10/23/91, imidazole solvation and sublimation<br></blockquote><blockquote type="cite">CT3c 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000<br></blockquote><blockquote type="cite">! ALLOW ALI<br></blockquote><blockquote type="cite"> ! methane/ethane a.i. and ethane pure solvent, adm jr,<br></blockquote><blockquote type="cite">2/3/92<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">Hch -2.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC<br></blockquote><blockquote type="cite"> ! same as TIP3P hydrogen, adm jr., 7/20/89<br></blockquote><blockquote type="cite">HAc 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC<br></blockquote><blockquote type="cite"> ! methane/ethane a.i. and ethane pure solvent, adm jr,<br></blockquote><blockquote type="cite">2/3/92<br></blockquote><blockquote type="cite">HA1c 0.000000 -0.031000 1.250000 !<br></blockquote><blockquote type="cite"> ! for propene, yin/adm jr., 12/95<br></blockquote><blockquote type="cite">HPc 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200<br></blockquote><blockquote type="cite">! ALLOW ARO<br></blockquote><blockquote type="cite"> ! JES 8/25/89 values from Jorgensen fit to hydration energy<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">NR1c 0.000000 -0.200000 1.850000 ! ALLOW ARO<br></blockquote><blockquote type="cite"> ! His, adm jr., 9/4/89<br></blockquote><blockquote type="cite">NR2c 0.000000 -0.200000 1.850000 ! ALLOW ARO<br></blockquote><blockquote type="cite"> ! His, adm jr., 9/4/89<br></blockquote><blockquote type="cite">!<br></blockquote><blockquote type="cite">!Och 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000<br></blockquote><blockquote type="cite">! ALLOW PEP POL<br></blockquote><blockquote type="cite">! ! This 1,4 vdW allows the C5 dipeptide minimum to<br></blockquote><blockquote type="cite">exist.(LK)<br></blockquote><blockquote type="cite">Och 0.000000 -0.120000 1.700000! ALLOW PEP POL, suppression du<br></blockquote><blockquote type="cite">terme 1,4 (N.R. 10/2000)<br></blockquote><blockquote type="cite">OHc 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO<br></blockquote><blockquote type="cite"> ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use<br></blockquote><blockquote type="cite"> ! READ PARAM APPEND CARD<br></blockquote><blockquote type="cite"> ! to append hbond parameters from the file: par_hbond.inp<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">END<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">Bharat<br></blockquote><blockquote type="cite">Ph.D. Candidate<br></blockquote><blockquote type="cite">Room No. : 7202A, 2nd Floor<br></blockquote><blockquote type="cite">Biomolecular Engineering Laboratory<br></blockquote><blockquote type="cite">Division of Chemical Engineering and Polymer Science<br></blockquote><blockquote type="cite">Pusan National University<br></blockquote><blockquote type="cite">Busan -609735<br></blockquote><blockquote type="cite">South Korea<br></blockquote><blockquote type="cite">Lab phone no. - +82-51-510-3680, +82-51-583-8343<br></blockquote><blockquote type="cite">Mobile no. - 010-5818-3680<br></blockquote><blockquote type="cite">E-mail : <a href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a><br></blockquote></div></blockquote><div><br></div><div><br></div><br><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; 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">Stockholm Center for Biomembrane Research (CBR),</font></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Stockholm Bioinformatics Center (SBC),</p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Department of Biochemistry and Biophysics (DBB),</p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Stockholm University</p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br class="webkit-block-placeholder"></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Tel:<span class="Apple-converted-space"> </span><span class="Apple-tab-span" style="white-space: pre; ">        </span>+46-8-16 2746<span class="Apple-tab-span" style="white-space: pre; ">        </span><span class="Apple-tab-span" style="white-space: pre; ">        </span><span class="Apple-tab-span" style="white-space: pre; ">        </span></font></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Fax:<span class="Apple-converted-space"> </span>+46-8-15 3679<span class="Apple-tab-span" style="white-space: pre; ">        </span><span class="Apple-tab-span" style="white-space: pre; ">        </span><span class="Apple-tab-span" style="white-space: pre; ">        </span></font></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">E-mail: <a href="mailto:bjelkmar@cbr.su.se">bjelkmar@cbr.su.se</a><span class="Apple-tab-span" style="white-space: pre; ">        </span><span class="Apple-tab-span" style="white-space: pre; "></span></font></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Home: <span class="Apple-tab-span" style="white-space: pre; "><span class="Apple-style-span" style="white-space: normal; "><a href="http://www.dbb.su.se/User:Bjelkmar">http://www.dbb.su.se/User:Bjelkmar</a><span class="Apple-tab-span" style="white-space: pre; ">        </span><span class="Apple-tab-span" style="white-space: pre; ">        </span></span></span></font></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; "><><><><><><><><><><><><><><><><><><><><><></font></p></div></div></span></div></span></div></span></div></span></div></span></div></span></span>
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