Hi,<div><br></div><div>I have obtained the chromophore parameters of the GFP for charmm force field but I am not able to find it out how to add it to the charmm FF file.. I have two files one is the topology file , which looks like this :- </div>
<div><p class="MsoPlainText"><span style="font-family:"Courier New"">*<br>
<span style="mso-spacerun:yes"> </span>22 <span style="mso-spacerun:yes"> </span>1<br>
MASS<span style="mso-spacerun:yes"> </span>13 CP2c<span style="mso-spacerun:yes"> </span>12.01100 C ! his CE1 carbon<br>
MASS<span style="mso-spacerun:yes"> </span>14 NR2c<span style="mso-spacerun:yes"> </span>14.00700 N ! neutral his unprotonated ring
nitrogen<br>
MASS<span style="mso-spacerun:yes"> </span>15 NR1c<span style="mso-spacerun:yes"> </span>14.00700 N ! neutral his protonated ring
nitrogen<br>
MASS<span style="mso-spacerun:yes"> </span>16 CP1c<span style="mso-spacerun:yes"> </span>12.01100 C ! his CG and CD2 carbons<br>
MASS<span style="mso-spacerun:yes"> </span>17 Och<span style="mso-spacerun:yes"> </span>15.99900 O ! carbonyl oxygen<br>
MASS<span style="mso-spacerun:yes"> </span>18 CE1c<span style="mso-spacerun:yes"> </span>12.01100 C ! for alkene; RHC=CR<br>
MASS<span style="mso-spacerun:yes"> </span>19 HA1c<span style="mso-spacerun:yes"> </span>1.00800 H ! for alkene; RHC=CR<br>
MASS<span style="mso-spacerun:yes"> </span>41 CA4<span style="mso-spacerun:yes"> </span>12.01100 C ! aromatic C<br>
MASS<span style="mso-spacerun:yes"> </span>42 HPc<span style="mso-spacerun:yes"> </span>1.00800 H ! aromatic H<br>
MASS<span style="mso-spacerun:yes"> </span>43 OHc<span style="mso-spacerun:yes"> </span>15.99900 O ! from OH1<br>
MASS<span style="mso-spacerun:yes"> </span>44 Hch<span style="mso-spacerun:yes"> </span>1.00800 H ! polar H<br>
MASS<span style="mso-spacerun:yes"> </span>45 CT3c<span style="mso-spacerun:yes"> </span>12.01100 C ! aliphatic sp3 C for CH3<br>
MASS<span style="mso-spacerun:yes"> </span>46 HAc<span style="mso-spacerun:yes"> </span>1.00800 H ! nonpolar H<br>
MASS<span style="mso-spacerun:yes"> </span>47 CA1<span style="mso-spacerun:yes"> </span>12.01100 C ! aromatic C<br>
MASS<span style="mso-spacerun:yes"> </span>48 CA2<span style="mso-spacerun:yes"> </span>12.01100 C ! aromatic C<br>
MASS<span style="mso-spacerun:yes"> </span>49 CA3<span style="mso-spacerun:yes"> </span>12.01100 C ! aromatic C<br>
<br>
DECL -CA<br>
DECL -C<br>
DECL -O<br>
DECL +N<br>
DECL +HN<br>
DECL +CA<br>
DEFA FIRS NTER LAST CTER<br>
AUTO ANGLES DIHE<br>
<br>
<br>
AUTOGENERATE ANGLES DIHE<br>
DEFA FIRS NONE LAST NONE<br>
<br>
RESI CRO<span style="mso-spacerun:yes"> </span>0.000<br>
GROUP<span style="mso-spacerun:yes"> </span>! Imidazolinone
ring<br>
ATOM C1 CP2c<span style="mso-spacerun:yes"> </span>0.76<br>
ATOM N2 NR2c -0.55<br>
ATOM N3 NR1c -0.64<br>
ATOM C2 CP1c<span style="mso-spacerun:yes"> </span>0.80<br>
ATOM O2 Och<span style="mso-spacerun:yes"> </span>-0.61<br>
ATOM CA CP1c<span style="mso-spacerun:yes"> </span>0.24<br>
!<br>
GROUP<span style="mso-spacerun:yes"> </span>! Charges from
propene<br>
ATOM CB CE1c -0.10<br>
ATOM HB HA1c<span style="mso-spacerun:yes"> </span>0.10<br>
!<br>
GROUP<span style="mso-spacerun:yes"> </span>! Tyr ring :
charges from charmm22<br>
ATOM CG2 CA1<span style="mso-spacerun:yes"> </span>0.00<br>
ATOM CD1 CA2<span style="mso-spacerun:yes"> </span>-0.115<br>
ATOM HD1 HPc<span style="mso-spacerun:yes"> </span>0.115<br>
ATOM CD2 CA2<span style="mso-spacerun:yes"> </span>-0.115<br>
ATOM HD2 HPc<span style="mso-spacerun:yes"> </span>0.115<br>
ATOM CE1 CA3<span style="mso-spacerun:yes"> </span>-0.115<br>
ATOM HE1 HPc<span style="mso-spacerun:yes"> </span>0.115<br>
ATOM CE2 CA3<span style="mso-spacerun:yes"> </span>-0.115 <br>
ATOM HE2 HPc<span style="mso-spacerun:yes"> </span>0.115<br>
ATOM CZ CA4<span style="mso-spacerun:yes"> </span>0.11<br>
ATOM OH Ohc<span style="mso-spacerun:yes"> </span>-0.54<br>
ATOM HH Hch<span style="mso-spacerun:yes"> </span>0.43<br>
!<br>
!Glycine part / C=O taken from Charmm22<br>
GROUP<br>
ATOM CAg<span style="mso-spacerun:yes"> </span>CT2<span style="mso-spacerun:yes"> </span>-0.18<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>|<br>
ATOM HA1<span style="mso-spacerun:yes"> </span>HB<span style="mso-spacerun:yes"> </span>0.09<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>|<br>
ATOM HA2<span style="mso-spacerun:yes"> </span>HB<span style="mso-spacerun:yes"> </span>0.09<span style="mso-spacerun:yes">
</span>! HA1-CA-HA2<br>
GROUP<span style="mso-spacerun:yes"> </span>!<span style="mso-spacerun:yes"> </span>|<br>
ATOM C<span style="mso-spacerun:yes"> </span>C<span style="mso-spacerun:yes"> </span>0.51<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>|<br>
ATOM O<span style="mso-spacerun:yes"> </span>O<span style="mso-spacerun:yes"> </span>-0.51<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>C=O<br>
!<br>
!Serine part / taken from Charmm22<br>
GROUP<br>
ATOM N <span style="mso-spacerun:yes"> </span>NH1<span style="mso-spacerun:yes"> </span>-0.47<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>|<br>
ATOM HN<span style="mso-spacerun:yes"> </span>H<span style="mso-spacerun:yes"> </span>0.31<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>HN-N<br>
ATOM CAs<span style="mso-spacerun:yes"> </span>CT1<span style="mso-spacerun:yes"> </span>0.07<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>|<span style="mso-spacerun:yes"> </span>HB1<br>
ATOM HA<span style="mso-spacerun:yes"> </span>HB<span style="mso-spacerun:yes"> </span>0.09<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>|<span style="mso-spacerun:yes"> </span>|<br>
GROUP<span style="mso-spacerun:yes"> </span>!<span style="mso-spacerun:yes"> </span>HA-CA--CB--OG<br>
ATOM CBs<span style="mso-spacerun:yes"> </span>CT2<span style="mso-spacerun:yes"> </span>0.05<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>|<span style="mso-spacerun:yes"> </span>|<span style="mso-spacerun:yes">
</span>\<br>
ATOM HB1<span style="mso-spacerun:yes"> </span>HA<span style="mso-spacerun:yes"> </span>0.09<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>|<span style="mso-spacerun:yes"> </span>HB2<span style="mso-spacerun:yes">
</span>HG1<br>
ATOM HB2<span style="mso-spacerun:yes"> </span>HA<span style="mso-spacerun:yes"> </span>0.09<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>O=C<br>
ATOM OG1<span style="mso-spacerun:yes"> </span>OH1<span style="mso-spacerun:yes"> </span>-0.66<span style="mso-spacerun:yes">
</span>!<span style="mso-spacerun:yes"> </span>|<br>
ATOM HG1<span style="mso-spacerun:yes"> </span>H<span style="mso-spacerun:yes"> </span>0.43<br></span></p></div><div> </div><div><br></div><div><br></div><div>Other file is the parameter file :-</div><div><br></div>
<div><div>! GFP Chromophore parameters, protonated form</div><div>!</div><div>BONDS</div><div>!</div><div>!V(bond) = Kb(b - b0)**2</div><div>!</div><div>!Kb: kcal/mole/A**2</div><div>!b0: A</div><div>!</div><div>!atom type Kb b0</div>
<div>CA1 CA2 305.00 1.3750 !</div><div>CA2 CA3 305.00 1.3750 !</div><div>CA3 CA4 305.00 1.3750 !</div><div>HPc CA1 340.000 1.08 !</div><div>HPc CA2 340.000 1.08 !</div><div>HPc CA3 340.000 1.08 !</div>
<div>HPc CA4 340.000 1.08 !</div><div>Ohc Hch 545 0.96 ! </div><div>Ohc CA4 334.3 1.4110 !</div><div>HA1c CE1c 360.500 1.10 ! </div><div>NR1c CP1c 400.000 1.41 !</div><div>NR1c CP2c 400.000 1.39 ! </div>
<div>NR2c CP2c 400.000 1.30 ! </div><div>NR2c CP1c 400.000 1.40 !</div><div>CP1c CP1c 410.000 1.49 !</div><div>CP1c CE1c 560 1.36 !</div><div>CP1c Och 807 1.22 !</div><div>CE1c CA1 370 1.45 !</div>
<div>NR1c CT2 352 1.45 ! </div><div>CP2c CT1 320 1.49 ! </div><div><br></div><div><br></div><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>OcH CP1c CP1c 38.00 132.00 !</div><div>CP1c CP1c CE1c 45.80 122.00 ! </div><div>CP1c CE1c CA1 130.00 130.00 ! </div>
<div>CP1c CE1c HA1c 42.00 114.00 ! </div><div>CE1c CA1 CA2 45.80 121.00 </div><div>HA1c CE1c CA1 42.00 116.00 ! </div><div>CA1 CA2 CA3 40.000 120.00 35.00 2.41620</div><div>CA2 CA1 CA2 40.000 120.00 35.00 2.41620</div>
<div>CA2 CA3 CA4 40.000 120.00 35.00 2.41620</div><div>CA3 CA4 CA3 40.000 120.00 35.00 2.41620</div><div>!</div><div>HPc CA3 CA4 30.000 120.00 22.00 2.15250 </div><div>HPc CA3 CA2 30.000 120.00 22.00 2.15250</div>
<div>HPc CA2 CA3 30.000 120.00 22.00 2.15250</div><div>HPc CA2 CA1 30.000 120.00 22.00 2.15250</div><div>!</div><div>Ohc CA4 CA3 45.200 120.0000 ! ALLOW ARO ALC</div><div>HcH Ohc CA4 65.000 108.0000 ! ALLOW ALC ARO</div>
<div>!</div><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>NR1C CP2C CT1 35.00 121.40 ! </div><div>!</div><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>CA2 CA1 CA2 CA3 3.1000 2 180.00 ! </div><div>CA2 CA3 CA4 CA3 3.1000 2 180.00 ! </div>
<div>!OCh CAC CAC CAC 3.1000 2 180.00 ! </div><div>CA2 CA3 CA4 OhC 3.1000 2 180.00 ! </div><div>CA1 CA2 CA3 HPC 4.2000 2 180.00 ! </div><div>CA2 CA1 CA2 HPC 4.2000 2 180.00 ! </div>
<div>CA3 CA4 CA3 HPC 4.2000 2 180.00 ! </div><div>HPC CA2 CA3 CA4 4.2000 2 180.00 ! </div><div>HPC CA2 CA3 HPC 2.4000 2 180.00 ! </div><div>!HCH OCh CAC CAC 0.9900 2 180.00 ! </div>
<div>HCH OhC CA4 CA3 0.9900 2 180.00 ! </div><div>HPC CA3 CA4 OhC 4.2000 2 180.00 ! </div><div>!</div><div>CP2C NR2C CP1C CE1C 3.000 2 180.00 ! </div><div>NR1C CP1C CP1C CE1C 3.00 2 180.00 ! </div>
<div>OCH CP1C CP1C CE1C 2.00 2 180.00 ! </div><div>CE1C CA1 CA2 HPC 4.20 2 180.00 ! </div><div>CE1C CA1 CA2 CA3 3.10 2 180.00 ! </div><div>!</div><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>NR1C CP2C CT1 NH1 0.105 3 0.00 ! </div>
<div>NR1C CP2C CT1 CT2 0.105 3 0.00 ! </div><div><br></div><div><br></div><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><div>CE1C CP1C CA1 HA1C 30.0 0 0.00</div><div>CE1C CA1 CP1C HA1C 30.0 0 0.00</div>
<div><br></div><div><br></div><div>Can anybody jus tell it how to do .. as I have posted this question earlier in the forum and got chapter 5 to read as suggestion ?? ... but I am a bit confused ...how to do it </div><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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