remarks file generate/generateco.inp remarks Sample: generate protein structure with a cofactor. Equilibrium remarks (target) parameters for the co-factor are learned from Cartesian remarks coordinates. Protein parameters are obtained from the standard remarks "parhcsdx.pro" parameter set. topology @TOPPAR:tophcsdx.pro autogenerate angles=true end {* Define default mass for P. The other masses *} {* are already defined in file "tophcsdx.pro". *} MASS P 30.97400 RESIdue PMP {* Pyridoxamine phosphate; the *} {* name PMP has to match what is *} {* used in the coordinate file. *} GROUP {* All PMP charges are set to 0 which is appropriate *} {* for refinement purposes. The PMP atom types are *} {* used for assigning the default mass for each *} {* atom. The PMP atom types are unimportant for *} {* the parameterization since the parameters are *} {* learned from the PMP coordinates. *} ATOM P TYPE=P CHARge=0. END ATOM OP1 TYPE=O CHARge=0. END ATOM OP2 TYPE=O CHARge=0. END ATOM OP3 TYPE=O CHARge=0. END ATOM OP4 TYPE=O CHARge=0. END GROUP ATOM C5A TYPE=CH2E CHARge=0. END ATOM C5 TYPE=C CHARge=0. END GROUP ATOM N1 TYPE=NH2 CHARge=0. END ATOM C6 TYPE=CH1E CHARge=0. END GROUP ATOM C2 TYPE=C CHARge=0. END ATOM C2A TYPE=CH3E CHARge=0. END GROUP ATOM C3 TYPE=C CHARge=0. END ATOM O3 TYPE=O CHARge=0. END ATOM H3 TYPE=H CHARge=0. END GROUP ATOM C4 TYPE=C CHARge=0. END ATOM C4A TYPE=CH2E CHARge=0. END GROUP ATOM N4 TYPE=MMM CHARge=0. END ATOM H41 TYPE=H CHARge=0. END ATOM H42 TYPE=H CHARge=0. END BOND P OP1 BOND P OP2 BOND P OP3 BOND P OP4 BOND OP4 C5A BOND C5A C5 BOND N1 C2 BOND N1 C6 BOND C2 C2A BOND C2 C3 BOND C3 O3 BOND O3 H3 BOND C3 C4 BOND C4 C4A BOND C4A N4 BOND N4 H41 BOND N4 H42 BOND C4 C5 BOND C5 C6 {* Impropers are specified to define groups of *} {* atoms with rigid planar or tetrahedral geometry. *} IMPRoper N1 C2 C3 C4 IMPRoper C2 C3 C4 C5 IMPRoper C3 C4 C5 C6 IMPRoper C4 C5 C6 N1 IMPRoper C5 C6 N1 C2 IMPRoper C6 N1 C2 C3 IMPRoper O3 C2 C4 C3 IMPRoper C2A N1 C3 C2 IMPRoper C5A C4 C6 C5 IMPRoper C4A C3 C5 C4 IMPRoper H42 C4A H41 N4 end end {*Generate protein.*} segment name=" " chain @TOPPAR:toph19.pep coordinates @../generate/maat.pdb end end {*Rename atoms. *} vector do (name="O") ( name OT1 ) vector do (name="OT") ( name OT2 ) vector do (name="CD1") ( name CD and resname ile ) coordinates @../generate/maat.pdb {*Generate PMP.*} segment name=" " chain coordinates @../generate/maat.pmp end end coordinates @../generate/maat.pmp parameter @TOPPAR:parhcsdx.pro {* Learn parameters for PMP from the cartesian coordinates. *} {* Parameters involving hydrogens have to be set explicitly *} {* since the cartesian coordinates are unavailabe in this *} {* case. *} {* Learn equilibrium parameters from known cartesian coordinates. *} learn initiate sele=(resname PMP and known ) mode=nostatistics end learn accumulate end learn terminate end {* Set energy constants. We are using generic values. *} BOND (resname PMP ) (resname PMP ) 500. TOKEN ANGLE (resname PMP ) (resname PMP ) (resname PMP ) 500. TOKEN IMPR (resname PMP ) (resname PMP ) (resname PMP ) (resname PMP ) 500. TOKEN TOKEN {* Set nonbonded parameters (epsilon and sigma) *} {* for the Lennard-Jones potential. *} NONBonded ( name C* and resname PMP ) 0.1 3.5 0.1 3.5 NONBonded ( name H* and resname PMP ) 0.05 1.4 0.05 1.4 NONBonded ( name O* and resname PMP ) 0.1 3.4 0.1 3.4 NONBonded ( name N* and resname PMP ) 0.1 3.4 0.1 3.4 NONBonded ( name P* and resname PMP ) 0.58 3.38 0.58 3.38 {* Set equilibrium parameters for hydrogens bonded to heavy atoms. *} {* These parameters are needed for the hydrogen building procedure.*} {* Once the hydrogens have been built, the following statement are *} {* not required in subsequent jobs. *} BOND (name H* and resn PMP ) (resn PMP ) 500. 1. ANGLE (name H4* and resn PMP ) (resn PMP ) (resn PMP ) 500. 120. ANGLE (name H3 and resn PMP ) (resn PMP ) (resn PMP ) 500. 110. end flags exclude vdw elec impr end {* Do quick hydrogen building without *} {* nonbonded interactions. Impropers*} {* are excluded as well to avoid *} {* problems with unknown parameters. *} hbuild {* This statement builds missing *} selection=( hydrogen ) {* hydrogens. *} phistep=45 {* for the force field. *} end constraints fix=( not hydrogen ) end {* Minimize hydrogen positions. *} flags include vdw elec end minimize powell nstep=40 end constraints fix=( not all ) end write coordinates output=generateco.pdb end write structure output=generateco.psf end stop {* ----------------------------------------------------------------------- *} {* In all subsequent jobs one has to re-create the PMP parameters *} {* using the generated coordinates as a reference. All jobs must *} {* begin with the following statements: *} {===>} structure @generateco.psf end {* Read structure file. *} {===>} coor @generateco.pdb {* Read reference coordinates for learning. *} parameter @TOPPAR:parhcsdx.pro {* Learn parameters for PMP from the cartesian coordinates. *} {* Learn equilibrium parameters from known cartesian coordinates. *} learn initiate sele=(resname PMP and known ) mode=nostatistics end learn accumulate end learn terminate end {* Set energy constants. We are using generic values. *} BOND (resname PMP ) (resname PMP ) 500. TOKEN ANGLE (resname PMP ) (resname PMP ) (resname PMP ) 500. TOKEN IMPR (resname PMP ) (resname PMP ) (resname PMP ) (resname PMP ) 500. TOKEN TOKEN {* Set nonbonded parameters (epsilon and sigma) *} {* for the Lennard-Jones potential. *} NONBonded ( name C* and resname PMP ) 0.1 3.5 0.1 3.5 NONBonded ( name H* and resname PMP ) 0.05 1.4 0.05 1.4 NONBonded ( name O* and resname PMP ) 0.1 3.4 0.1 3.4 NONBonded ( name N* and resname PMP ) 0.1 3.4 0.1 3.4 NONBonded ( name P* and resname PMP ) 0.58 3.38 0.58 3.38 end {===>} coor @generateco.pdb {* Read current coordinates.*} {* Now the parameters are well-defined and one can proceed with *} {* any X-PLOR task. *}