Hi,<div><br></div><div>I followed the tutorial - <span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "><a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" target="_blank" style="color: rgb(0, 0, 204); ">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a> for updating the Charmm FF for my modified residue ..</span></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">I added the residues to the .rtp file , then I added the new atom types in .atp file , </span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">(The parameter file of the compound looks like this ) ..</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"> </span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><div style="border-collapse: collapse; ">
BONDS</div><div style="border-collapse: collapse; ">!</div><div style="border-collapse: collapse; ">!V(bond) = Kb(b - b0)**2</div><div style="border-collapse: collapse; ">!</div><div style="border-collapse: collapse; ">!Kb: kcal/mole/A**2</div>
<div style="border-collapse: collapse; ">!b0: A</div><div style="border-collapse: collapse; ">!</div><div style="border-collapse: collapse; ">!atom type Kb b0</div><div style="border-collapse: collapse; ">CA1 CA2 305.00 1.3750 !</div>
<div style="border-collapse: collapse; ">CA2 CA3 305.00 1.3750 !</div><div style="border-collapse: collapse; ">CA3 CA4 305.00 1.3750 !</div><div style="border-collapse: collapse; ">HPc CA1 340.000 1.08 !</div>
<div style="border-collapse: collapse; ">HPc CA2 340.000 1.08 !</div><div style="border-collapse: collapse; ">HPc CA3 340.000 1.08 !</div><div style="border-collapse: collapse; ">HPc CA4 340.000 1.08 !</div>
<div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; "><div>ANGLES</div><div>!</div><div>!V(angle) = Ktheta(Theta - Theta0)**2</div><div>
!</div><div>!V(Urey-Bradley) = Kub(S - S0)**2</div><div>!</div><div>!Ktheta: kcal/mole/rad**2</div><div>!Theta0: degrees</div><div>!Kub: kcal/mole/A**2 (Urey-Bradley)</div><div>!S0: A</div><div>!</div><div>!atom types Ktheta Theta0 Kub S0</div>
<div>!</div><div>NR2c CP2c NR1c 130.00 114.00 ! </div><div>CP2c NR2c CP1c 130.00 106.00 ! </div><div>CP2c NR1c CP1c 130.00 107.90 ! </div><div>NR2c CP1c CP1c 130.00 108.30 ! </div><div>NR2c CP1c CE1c 45.80 129.50 ! </div>
<div>NR1c CP1c OcH 42.00 126.00 !</div><div>NR1c CP1c CP1c 130.00 103.00 ! </div></div><div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; ">
<div>!Connection to the ser fragment</div><div>!------------------------------</div><div>CT2 CT1 CP2c 52.000 108.0000 ! ALLOW ALI PEP POL ARO</div><div>HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP</div><div>NH1 CT1 CP2c 50.000 107.0000 ! ALLOW PEP POL ARO ALI</div>
<div>NR2C CP2C CT1 40.00 125.00 ! </div></div><div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; ">
<div>!Connection to the gly fragment</div><div>!------------------------------</div><div>NR1C CT2 C 50.000 107.0000 </div><div>NR1c CT2 HB 48.000 108.0000</div><div>CP2C NR1C CT2 36.00 129.00</div><div>
CP1C NR1C CT2 32.00 123.40</div><div>!</div><div>DIHEDRALS</div><div>!</div><div>!V(dihedral) = Kchi(1 + cos(n(chi) - delta))</div><div>!</div><div>!Kchi: kcal/mole</div><div>!n: multiplicity</div><div>!delta: degrees</div>
<div>!</div><div>!atom types Kchi n delta</div><div>!</div><div>CP2C NR2C CP1C CP1C 14.0000 2 180.00 ! </div><div>CP2C NR1C CP1C CP1C 14.0000 2 180.00 !</div><div>NR2C CP2C NR1C CP1C 14.0000 2 180.00 !</div>
<div>NR2C CP1C CP1C NR1C 4.0000 2 180.00 ! </div><div>NR1C CP2C NR2C CP1C 4.0000 2 180.00 ! </div><div>CA1 CA2 CA3 CA4 3.1000 2 180.00 ! </div></div><div style="border-collapse: collapse; "><br></div>
<div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; "><div>!barrier CA-CB</div><div>CP1C CP1C CE1C HA1C 6.84 2 180.00 ! </div><div>CP1C CP1C CE1C CA1 6.84 2 180.00 !</div>
<div>NR2C CP1C CE1C HA1C 6.84 2 180.00 !</div><div>NR2C CP1C CE1C CA1 6.84 2 180.00 ! </div><div>!</div><div>!barrier CB-CG2</div><div>CP1C CE1C CA1 CA2 1.4 2 180.00 ! </div><div>HA1C CE1C CA1 CA2 1.4 2 180.00 ! </div>
<div>!</div><div>CP2C NR1C CP1C OCH 14.00 2 180.00 !</div><div>NR2C CP2C NR1C CT2 14.00 2 180.00 !</div><div>NR2C CP1C CP1C OCH 14.00 2 180.00 !</div><div>CP1C NR1C CP2C CT1 14.00 2 180.00 !</div>
<div>OCH CP1C NR1C CT2 14.00 2 180.00 !</div><div>CP1C NR2C CP2C CT1 14.00 2 180.00 !</div><div>CP1C CP1C NR1C CT2 14.00 2 180.00 !</div><div>CT1 CP2C NR1C CT2 14.00 2 180.00 !</div>
<div>!</div><div>! Linking the chromophore and the glycine fragment</div><div>O C CT2 NR1C 0.0000 1 0.00 ! </div><div>NH1 C CT2 NR1c 0.6000 1 0.00 ! </div><div>CP2C NR1C CT2 HB 0.032 3 0.00 ! </div>
<div>CP2c NR1c CT2 C 0.032 3 0.00 !</div><div>CP1c NR1c CT2 HB 0.032 3 180.00 !</div><div>CP1c NR1c CT2 C 0.032 3 180.00 !</div><div>!</div><div>! Linking the chromophore and the serine fragment</div>
<div>C NH1 CT1 CP2C 0.2000 1 180.00 !</div><div>H NH1 CT1 CP2C 0.0000 1 0.00 !</div><div>NR2C CP2C CT1 HB 0.105 3 180.00 ! </div><div>NR2C CP2C CT1 NH1 0.105 3 180.00 ! </div>
<div>NR2C CP2C CT1 CT2 0.105 3 180.00 ! </div><div>NR1C CP2C CT1 HB 0.105 3 0.00 ! </div></div><div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; "><br></div>
<div style="border-collapse: collapse; "><div>IMPROPER</div><div>!</div><div>!V(improper) = Kpsi(psi - psi0)**2</div><div>!</div><div>!Kpsi: kcal/mole/rad**2</div><div>!psi0: degrees</div><div>!note that the second column of numbers (0) is ignored</div>
<div>!</div><div>!atom types Kpsi psi0</div><div>!</div><div>CP2C NR2C NR1C CT1 0.5 0 0.00</div><div>CP2C NR1C NR2C CT1 0.5 0 0.00</div><div>!</div><div>
CP1C NR1C CP1C OCH 0.5 0 0.00</div><div>CP1C CP1C NR1C OCH 0.5 0 0.00</div><div>!</div><div>NR1C CP1C CP2C CT2 0.45 0 0.00 </div><div>NR1C CP2C CP1C CT2 0.45 0 0.00 </div>
<div>!</div><div>CP1C NR2C CP1C CE1C 220.0 0 0.00</div><div>CP1C CP1C NR2C CE1C 220.0 0 0.00</div></div><div style="border-collapse: collapse; "><br></div><div style="border-collapse: collapse; ">
<br></div><div><div><span class="Apple-style-span" style="border-collapse: collapse;">!</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">!</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)</span></div><div>
<span class="Apple-style-span" style="border-collapse: collapse;">!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">!</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">!</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">!CAc 5.000000 -0.070000 1.992400 ! ALLOW ARO</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">! ! benzene (JES)</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">CA1 5.000000 -0.070000 1.992400 ! ALLOW ARO</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">CA2 5.000000 -0.070000 1.992400 ! ALLOW ARO</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">CA3 5.000000 -0.070000 1.992400 ! ALLOW ARO</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">CA4 5.000000 -0.070000 1.992400 ! ALLOW ARO</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">CE1c 0.000000 -0.068000 2.090000 ! </span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-tab-span" style="white-space:pre"> </span>! for propene, yin/adm jr., 12/95</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">CP1c 0.000000 -0.050000 1.800000 ! ALLOW ARO</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"> ! adm jr., 10/23/91, imidazole solvation and sublimation</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">CP2c 0.000000 -0.050000 1.800000 ! ALLOW ARO</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"> ! adm jr., 10/23/91, imidazole solvation and sublimation</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">CT3c 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"> ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">!</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">Hch -2.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;"> ! same as TIP3P hydrogen, adm jr., 7/20/89</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">HAc 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;"> ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">HA1c 0.000000 -0.031000 1.250000 !</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;"> ! for propene, yin/adm jr., 12/95</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">HPc 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;"> ! JES 8/25/89 values from Jorgensen fit to hydration energy</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">!</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">NR1c 0.000000 -0.200000 1.850000 ! ALLOW ARO</span></div><div>
<span class="Apple-style-span" style="border-collapse: collapse;"> ! His, adm jr., 9/4/89</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">NR2c 0.000000 -0.200000 1.850000 ! ALLOW ARO</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"> ! His, adm jr., 9/4/89</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">!</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">!Och 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">! ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">Och 0.000000 -0.120000 1.700000! ALLOW PEP POL, suppression du terme 1,4 (N.R. 10/2000)</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;">OHc 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;"> ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P)</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"> ! READ PARAM APPEND CARD</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;"> ! to append hbond parameters from the file: par_hbond.inp</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">END</span></div></div><div style="border-collapse: collapse; ">
<br></div></font><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>Busan -609735<br>
South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>
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