<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt">My way of doing it is:<br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">(1) add two new residues entries (with two different names) for glycine and seine in the rtp file and corresponding FF files. The new entries in the rtp file for glycine and serine should have
the same number of atoms as in the real molecule (delete the unnecessary H
or OH groups if needed)<br>(2) then use pdb2gmx <br>(3) then manually construct the bond, angle and dihedrals at the linkage site. <br><br>Cheers,<br>Jianguo<br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> bharat gupta <bharat.85.monu@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thursday, 3 March 2011 11:31:38<br><b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] Re: adding ff parameter of modified residue to charmm ff<br></font><br><meta http-equiv="x-dns-prefetch-control" content="off">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
rel="nofollow" target="_blank" href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" 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>
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