Sirs,
I have mailed you sometime back but couldn't received reply, although I solved some problems, but still there are three of them which are hindering the work. It would be very kind if you suggest a solution to them.
Problems are:
1. What each column in *.D* file, which contains details about the optimization, represents? Also, does this file contains details of optimization of molecular pdf as well as Molecular Dynamics? and how to differentiate between them?
2. Running Modeler gives the following warnings:
Number of templates for coordinate transfer: 3 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 3290 1048 TOP_________> 146 87 BUILD_MODEL INITIALIZE_XYZ = OFF
build___466W> Some coordinates in MODEL not assigned. build___468W> Some coordinates in MODEL are still undefined. build___464W> Inventing the MODEL coordinates.
I understand that these atoms are undefined because it doesn't found equivalent atoms (same atom name and equivalent residue) in templates but then those atoms are given coordinates by BUILD_MODEL command, but can you tell me how one can find out which are those 'still' undefined atoms , even which are not covered by 'BUILD_MODEL' command and why this is so? Please explain this a bit.
3. Also, another problem is: New residue types defined in restyp as well as top_heav.lib. I am using this type of restyp.lib (residue defined for use in template)
141 | AAA | ? | A123 | residue XXX 142 | BBB | " | A234 | patch for residue XXX 143 | BBB | | A345 | patch for residue XXX
and alignment like
template : ----/"/----- target : ----/?/?----- (for this patches are defined explicitly by PATCH
command in top file)
this reads the first (") residue but doesn't read the next () residue and gives error: -------------
rdabrk__291E> Sequence difference between alignment and pdb :
STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES ------*---- 1 514 143 A345 141 A123 YVNLK" rdabrk__288W> Protein not accepted: 1 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
-------------
but when I change the PDB-3 name of residue from BBB to CCC in restyp.lib, then it works, but this needs me to change the residue name in PDB, but instructions of your restyp.lib suggests that same name of residue in PDB-3 are acceptable. Is this some type of probable bug? or I am doing some mistake? Also, patches are needed to be given some different PDB-1 and different CHARMM name, which I did.
Please reply, if you need more details, please say so.
Thanking you,
sincerely,
vivek sharma