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Generation and Manipulation of the Structure

The commands described in this node are used to construct and manipulate the PSF, the central data structure in CHARMM (see PSF.FCM). The PSF holds lists giving every bond, bond angle, torsion angle, and improper torsion angle as well as information needed to generate the hydrogen bonds and the non-bonded list. It is essential for the calculation of the energy of the system. A separate data structure deals with symmetric images of the atoms. See Images.

There is an order with which commands to generate and manipulate the PSF must be given. First, segments in the PSF must be generated one at a time. Prior to generating any segments, one must first have read a residue topology file, see Read. To generate one segment, one must first read in a sequence using the READ command, see Sequence. Then, the GENErate command must be given.

Once a segment is generated, it may be manipulated. This can be done in a very general way using the patch command. The patch command allows, for instance, the addition of disulfide bridges, changing the protonation state of a titratible residue or to make a histidine heme crosslink.

The PSF can be saved with the “WRITE PSF” command. A PSF may be read with the “READ PSF” command. The “READ PSF” command has an “APPEnd” option that allows the merging of individual PSF files. In addition, the “DELETE” command allows the deletetion of atoms and all references to the deleted atoms.

The Generate Command - Construct a Segment of the PSF

GENErate [segid] { generate-spec        } [SETUp]
                 {  DUPLicate segid     }

generate-spec::= [FIRSt pres] [LAST pres] [WARN] [ ANGLe   ] [ DIHEdrals ]
                                                 [ NOANgle ] [ NODIhedral]

This command uses the sequence of residues specified in the last READ SEQUuence command and the information stored in the residue topology file to add the next segment to the PSF. Each segment contains a list of all the bonds, angles, dihedral angles, and improper torsions needed to calculate the energy. It also assigns charges to all the atoms, sets up the nonbonded exclusions list, and specifies hydrogen bond donors and acceptors. Any internal coordinate which references atoms outside the range of the segment is deleted. This prevents any unexpected bonding of segments.

The FIRSt and LAST specifications define what patch-residues should be used for the terminating residues. If no specification is given, then the default patching as specified in the topology file will be used.

The WARN keyword, will list all elements that were deleted due to nonexistant atoms (usually references to the terminating residues).

The SETUp option will cause any internal coordinate table entries (IC) from the topology file to be appended to the main IC table.

The ANGLe (NOANgle) and DIHEdral (NODIhedral) options override the autogeneration option specified in the topology files. This may be done to suppress unwanted additional terms, or to add terms for specific residues.

Note

The solvent residues (TIP3, ST2, WAT) must be generated with the NOANgle and/or NODIhedral qualifier. This is only necessary for the files which use the AUTOgenerate ANGLes and/or DIHEdrals as a default. This also means that a protein residue sequence and water molecules may not be combined in the same generate command. Also, there is a special “READ SEQUence residue_type integer” command where integer is the number of resudies of residue_type (often water molecules). This avoids the need to list the number of residues followed by the specification of each TIP3 residue name individually as is done with a protein.

For the DUPLicate segment option, the generate command MUST NOT be preceded by a READ SEQUence command. This option will create a new segment which is identical (except for the segid) to an existing segment. This option is mainly intended for the use in setting up small crystals for viewing and other analysis.

Nonbonded Exclusion List (NBX)

Some pairs of atoms are excluded from the nbond exclusion lists because their interactions are described by other terms in the hamiltonian. By default directly bonded atoms and the 1-3 atoms of an angle are excluded from the nonbond calculation. In addition the diagonal interactions of the six membered rings in tyrosine and phenylalanine were excluded from the nonbond calculation through CHARMM version 15 with RTOPH6. Hydrogen bonds, and dihedral 1-4 interactions are not excluded (note that other workers may differ from us on one or both of these points).

The list of nonbonded exclusion is generated in two steps. First a preliminary list is made at generation by GENIC using any information that may be present in the topology file (for example, diagonal interactions in rings). The second step is an automatic compilation of all the bond and angle interactions, followed by a sorting of the list, performed in MAKINB. The list is stored in the linked list pair IBLO14/INB14, where IBLO14(i) points to the last exclusion in INB14 to atom i. If the list is modified after MAKINB, then either MAKINB should be called again to resort the list, or care must be taken to see that the INB14 list is ascending with all INB14 entries having higher atom numbers than i and that all atoms have at least one INB entry.

MAKINB is called by default after any operation which changes internal coordinates such as generate, patch, or edit.

The exclusion list can be specified in three ways. First, interactions that are to be excluded can be placed in the topology file by listing the excluded atoms after the charge. Second, NBXM mode can be specified as a qualifier to any of the commands which change internal coordinates. Third, the default NBXM value can be specified in the parameter file. The NBXM values and actions are (in the following “include” refers to what is being kept (included) in the exclusion list):

0 use the existing list (do nothing)
1 or -1 include nothing extra
2 or -2 include only 1-2 (bond) interactions
3 or -3 also include 1-3 (angle) interactions
4 or -4 also include 1-4 interactions automatically.
5 or -5 include up to 1-3 interactions as exclusions and process 1-4 interactions using the 1-4 van der Waal parameters and reduced elecrostatics (E14FAC).

Negative values suppress the use of the information present in the topology file. Positive values add to the information that was in the topology file.

Patch command to modify PSF

Syntax (command level)

PATCh <pres-name> segid1 resid1 [, segid2 resid2 [,...
                                 [, segid9 resid9]...]]
                                  [SORT]
                                   [SETUp]
                                    [WARN]

Syntax (corresponding patch residue in RTF)

   PRES <pres-name>

   [GROUp]
   [ATOM  <I><atomname>  <parameter type>   <charge> ]
   [DELEte ATOM <I><atomname>]

   [ [DELEte] BOND <I1> <I2> ]
   [ [DELEte] ANGLe <I1> <I2> <I3> ]
   [ [DELEte] DIHEdral <I1> <I2> <I3> <I4> ]
   [ [DELEte] IMPRoper <I1> <I2> <I3> <I4> ]
   [ [DELEte] DONOr  [<I1>] <I2> [[<I3> [<I4>]] ]
   [ [DELEte] ACCEptor  <I1> [ <I2> [ <I3> ]] ]

   [ IC  <I1> <I2> [*]<I3> <I4>   real real real real real ]
   [ DELEte IC <I1> <I2> [*]<I3> <I4> ]

where I1, I2, I3, I4 refer to <I><atomname>.

Rules governing the patch procedure:

  1. If an atom is being added via a PATCH at least one or more atoms already existing in the residue to which the patch is being added must be included in the PRES with an ATOM statement. Unless this(these) atoms are deleted using the DELEte ATOM command internal terms associated with this atom which are already present in the residue should NOT be included in the PRES.

  2. if no <I> is specified before <atomname> the patch procedure assumes that the atom should be in residue (segid1 resid1).

  3. a ‘-‘, ‘+’, ‘#’ as a first letter in <atomname> tries to locate or add the atom <atomname> in the previous, next, next of the next, residue of residue (segid<I> resid<I>), respectively.

  4. GROUP brackets in a patch residue have highest priority.

  5. If no GROUP is specified, the group numbers of referenced, already existing atoms remain unchanged. Added atoms are placed in the last group of the referenced residue.

  6. A GROUP statement in a patch residue CAN enclose atoms in different referenced residues. However, if there is a conflict between sequential residue AND group boundaries new residues MIGHT be created with resid’s and segid’s referring to the referenced residues. These cases are indicated by a message from MAPIC that a negative number of residues were created. The user has to check the PSF explicitly to decide whether the modifications done by PATCH are appropriate.

  7. Along with the PSF the coordinates, comparision coordinates, harmonic constraints, fixed atom list, internal coordinates (IC) are mapped correctly.

  8. THERE IS NO MAP OF NBONDS, HBONDS, SHAKE, DYNAMICS ETC. THE ATOMNUMBERS ARE CHANGED.

  9. Any bond, angle, etc referring to deleted atoms is itself deleted. The bond, angle, etc lists are compressed.

  10. Even if the AUTOgenerate ANGLe and/or DIHEdral option has been invoked new angles and/or dihedrals have to be included in the PRES when that particular patch is being called after the GENErate statement. The angles and/or dihedrals will be generated automatically for any patch which is called in the GENErate statement following the FIRSt or LAST statements. NOTE: If angles and dihedrals are present in a PRES which is called in a GENErate statement in which AUTOgenerate ANGLes and/or DIHEdrals is being used those angles and/or dihedrals will be invoked twice in the PSF and, thus, be included twice when the energy is calculated.

    The AUTOgenerate command (next) can be used to circumvent the above problems, and removes the need for specifying angles and dihedrals as part of a PRES definition.

Completely autogenerate all angles and/or dihedrals

AUTOgen   {  ANGLes     [ DIHEdrals ]  }
          {  DIHEdrals  [ ANGLes    ]  }

Sets the angle and/or dihedral counts to zero in the PSF, and rebuilds the indicated list(s) of energy terms. Intended to simplify the development of patches, since only bonding terms need to be specified in PRES definitions which are followed by this command. Note that at least one keyword is required, but both may be specified, in either order.

Warning

may be a problem if the PSF contains any water molecules.

Delete atoms or energy terms in the structure

DELEte  {   ATOMs        atom-selection                 } [SORT]
        {                                               }
        { { BONDs              } double-atom-selection  }
        { { ANGLes             }                        }
        { { DIHEdrals          }                        }
        { { IMPRoper-dihedrals }                        }
        { { CONNectivity       }                        }

The DELEte ATOM option deletes selected atoms and all references to them in PSF.

Note

THIS WILL CHANGE THE ATOM NUMBERING.

Note

If PERT is currently in use, this command only affects the active (lambda=1) PSF. The reference PSF (lambda=0) is only modified by the PERT command.

For the internal energy terms, any entry that has an atom selected in both atom selections will be deleted. Note, if an atom is selected in both atom selections, all connections to this atom will be deleted, except for bonds. For a bond to be deleted, one of its atoms must appear in each of the atom selections. The CONN (connectivity) option will delete all bond, angles, dihedrals, and improper dihedrals. This option avoids the necessity of running the DELEte command four times when one wishes to break some connectivity.

The SORT option performs an optional sorting of the PSF after the deleted atoms have been mapped out.

RENAme - rename portions of the current PSF

RENAme is invoked only from the main command parser and it includes the working PSF. Its syntax is;

RENAme  { SEGId }  new-name  atom-selection
        { RESId }
        { RESN  }
        { ATOM  }

Any atoms selected will have the corresponding ID modified. There is a check for duplicate SEGIDs, RESIDs, and atom names, but it wont stop you if BOMLEV is negative. Renaming ST2 will not change their status (except in the setup for SHAKE, which will be fixed soon).

Joining Two Adjacent Segments

For some operations, it is convenient to be able to join two adjacent segments together. This process has no effect on the energy terms, but just reorganizes naming and grouping of atoms into segments. This is especially useful with IMAGES so that all images in the PSF are identified only as a single segment.

JOIN  first_segment  [second_segment]  [ RENUmber ]

The second segment must follow the first sequentially in the PSF. There is no checking for duplicate residue identifiers. The RENUmber option sets the resid for each residue of the composite segment to the relative index in that segment (just as it would have during a generate command). If only a single segment is specified with the RENUmber option, then the resid’s of this segment will be numbered sequentially.