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solvate_stretch.log

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  1. [gtkleap]$ source leaprc.ff99SB
  2. logFile leap.log
  3. #
  4. # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
  5. # ----- this file is updated for PDB format 3
  6. #
  7. # load atom type hybridizations
  8. #
  9. addAtomTypes {
  10. { "H" "H" "sp3" }
  11. { "HO" "H" "sp3" }
  12. { "HS" "H" "sp3" }
  13. { "H1" "H" "sp3" }
  14. { "H2" "H" "sp3" }
  15. { "H3" "H" "sp3" }
  16. { "H4" "H" "sp3" }
  17. { "H5" "H" "sp3" }
  18. { "HW" "H" "sp3" }
  19. { "HC" "H" "sp3" }
  20. { "HA" "H" "sp3" }
  21. { "HP" "H" "sp3" }
  22. { "OH" "O" "sp3" }
  23. { "OS" "O" "sp3" }
  24. { "O" "O" "sp2" }
  25. { "O2" "O" "sp2" }
  26. { "OW" "O" "sp3" }
  27. { "CT" "C" "sp3" }
  28. { "CH" "C" "sp3" }
  29. { "C2" "C" "sp3" }
  30. { "C3" "C" "sp3" }
  31. { "C" "C" "sp2" }
  32. { "C*" "C" "sp2" }
  33. { "CA" "C" "sp2" }
  34. { "CB" "C" "sp2" }
  35. { "CC" "C" "sp2" }
  36. { "CN" "C" "sp2" }
  37. { "CM" "C" "sp2" }
  38. { "CK" "C" "sp2" }
  39. { "CQ" "C" "sp2" }
  40. { "CD" "C" "sp2" }
  41. { "CE" "C" "sp2" }
  42. { "CF" "C" "sp2" }
  43. { "CP" "C" "sp2" }
  44. { "CI" "C" "sp2" }
  45. { "CJ" "C" "sp2" }
  46. { "CW" "C" "sp2" }
  47. { "CV" "C" "sp2" }
  48. { "CR" "C" "sp2" }
  49. { "CA" "C" "sp2" }
  50. { "CY" "C" "sp2" }
  51. { "C0" "C" "sp2" }
  52. { "MG" "Mg" "sp3" }
  53. { "N" "N" "sp2" }
  54. { "NA" "N" "sp2" }
  55. { "N2" "N" "sp2" }
  56. { "N*" "N" "sp2" }
  57. { "NP" "N" "sp2" }
  58. { "NQ" "N" "sp2" }
  59. { "NB" "N" "sp2" }
  60. { "NC" "N" "sp2" }
  61. { "NT" "N" "sp3" }
  62. { "N3" "N" "sp3" }
  63. { "S" "S" "sp3" }
  64. { "SH" "S" "sp3" }
  65. { "P" "P" "sp3" }
  66. { "LP" "" "sp3" }
  67. { "F" "F" "sp3" }
  68. { "CL" "Cl" "sp3" }
  69. { "BR" "Br" "sp3" }
  70. { "I" "I" "sp3" }
  71. { "FE" "Fe" "sp3" }
  72. { "EP" "" "sp3" }
  73. # glycam
  74. { "OG" "O" "sp3" }
  75. { "OL" "O" "sp3" }
  76. { "AC" "C" "sp3" }
  77. { "EC" "C" "sp3" }
  78. }
  79. #
  80. # Load the main parameter set.
  81. #
  82. parm99 = loadamberparams parm99.dat
  83. frcmod99SB = loadamberparams frcmod.ff99SB
  84. #
  85. # Load DNA/RNA libraries
  86. #
  87. loadOff all_nucleic94.lib
  88. #
  89. # Load main chain and terminating
  90. # amino acid libraries (i.e. ff94 libs)
  91. #
  92. loadOff all_amino94.lib
  93. loadOff all_aminoct94.lib
  94. loadOff all_aminont94.lib
  95. #
  96. # Load water and ions
  97. #
  98. loadOff ions94.lib
  99. loadOff solvents.lib
  100. HOH = TP3
  101. WAT = TP3
  102. #
  103. # Define the PDB name map for the amino acids and DNA.
  104. #
  105. addPdbResMap {
  106. { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
  107. { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
  108. { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
  109. { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
  110. { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
  111. { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
  112. { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
  113. { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
  114. { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
  115. { 0 "HID" "NHID" } { 1 "HID" "CHID" }
  116. { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
  117. { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
  118. { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
  119. { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
  120. { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
  121. { 0 "MET" "NMET" } { 1 "MET" "CMET" }
  122. { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
  123. { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
  124. { 0 "SER" "NSER" } { 1 "SER" "CSER" }
  125. { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
  126. { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
  127. { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
  128. { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
  129. { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
  130. { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
  131. { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
  132. { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
  133. { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
  134. { 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" }
  135. { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" }
  136. { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" }
  137. { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" }
  138. { 0 "DG" "DG5" } { 1 "DG" "DG3" }
  139. { 0 "DA" "DA5" } { 1 "DA" "DA3" }
  140. { 0 "DC" "DC5" } { 1 "DC" "DC3" }
  141. { 0 "DT" "DT5" } { 1 "DT" "DT3" }
  142. }
  143. addPdbAtomMap {
  144. { "O5*" "O5'" }
  145. { "C5*" "C5'" }
  146. { "C4*" "C4'" }
  147. { "O4*" "O4'" }
  148. { "C3*" "C3'" }
  149. { "O3*" "O3'" }
  150. { "C2*" "C2'" }
  151. { "C1*" "C1'" }
  152. { "C5M" "C7" }
  153. { "O2*" "O2'" }
  154. { "H1*" "H1'" }
  155. { "H2*1" "H2'1" }
  156. { "H2*2" "H2'2" }
  157. { "H2'" "H2'1" }
  158. { "H2''" "H2'2" }
  159. { "H3*" "H3'" }
  160. { "H4*" "H4'" }
  161. { "H5*1" "H5'1" }
  162. { "H5*2" "H5'2" }
  163. { "H5'" "H5'1" }
  164. { "H5''" "H5'2" }
  165. { "HO2'" "HO'2" }
  166. { "HO5'" "H5T" }
  167. { "HO3'" "H3T" }
  168. { "O1'" "O4'" }
  169. { "OA" "O1P" }
  170. { "OB" "O2P" }
  171. { "OP1" "O1P" }
  172. { "OP2" "O2P" }
  173. }
  174. #
  175. # assumed that most often proteins use HIE
  176. #
  177. NHIS = NHIE
  178. HIS = HIE
  179. CHIS = CHIE
  180. [gtkleap]$ loadamberparams frcmod.spce
  181. [gtkleap]$ WAT = SPC
  182. [gtkleap]$ set WAT.1 name "SPC"
  183. [gtkleap]$ mol = loadpdb fcp1_stretch.pdb
  184. [gtkleap]$ addhydr mol
  185. [gtkleap]$ parmchk mol
  186. [gtkleap]$ saveamberparm mol fcp1_stretch.top fcp1_stretch.crd
  187. [gtkleap]$ addions mol Na+ 0
  188. Info: rmax, rion, shell: 2 1.868 4
  189. Info: pmin: -16.524 -20.177 -7.824
  190. Info: pmax: 32.675 29.437 21.039
  191. Info: enclosing: -24.392 -28.045 -15.692
  192. Info: to: 40.543 37.305 28.907
  193. Info: new ion will be placed at: 22.608 12.955 -3.692
  194. Info: new ion will be placed at: -0.392 -4.045 17.308
  195. Info: new ion will be placed at: -16.392 -22.045 21.308
  196. Info: new ion will be placed at: -1.392 -12.045 14.308
  197. Info: new ion will be placed at: 17.608 10.955 8.308
  198. [gtkleap]$ saveamberparm mol fcp1_stretch_ion.top fcp1_stretch_ion.crd
  199. [gtkleap]$ solvateoct mol SPCBOX 12.0 iso
  200. rgn size: 103.174 103.174 103.174
  201. svt size: 18.774 18.774 18.774
  202. nx,ny,nz: 6 6 6
  203. [gtkleap]$ savepdb mol fcp1_stretch_pme.pdb
  204. saving mol to fcp1_stretch_pme.pdb
  205. [gtkleap]$ saveamberparm mol fcp1_stretch_pme.top fcp1_stretch_pme.crd
  206. [gtkleap]$ quit
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