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wdy Offline
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I added FIRST NONE LAST NONE to the GENERATE commands, and It didn't result.
Second, I applied bomlev -5, to run the script anyway. I found only one maximum number that is no satisfied (MAXT). Here it's the output:

**** ERROR **** A COUNTER VARIABLE HAS EXCEEDED ITS MAXIMUM ALLOWABLE VALUE.
EXECUTION WILL BE TERMINATED.
THE CURRENT COUNTER VARIABLES AND THEIR MAXIMUM ALLOWED VALUES ARE:
NSEG = 4 MAXSEG = 1000 NATOM = 14460 MAXA = 25140 NBOND = 14660 MAXB = 25140
NTHETA = 26424 MAXT = 25140 NPHI = 38772 MAXP = 50280 NIMPHI = 2192 MAXIMP = 9200
NNB = 0 MAXNB = 17200 NDON = 1424 MAXPAD = 8160 NACC = 1228 MAXPAD = 8160
NRES = 884 MAXRES = 14000 NATC = 195 MAXATC = 500 NCB = 250 MAXCB = 1500
NCT = 622 MAXCT = 15500 NCP = 1049 MAXCP = 3000 NCI = 73 MAXCI = 600
NCH = 0 MAXCH = 3200 NCN = 8515 MAXCN = 20100

Is the number of angles the problem?


Wendy González Bioinformatics and Molecular Simulation Centre University of Talca Chile
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rmv Offline OP
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It does appear that you've exceeded MAXT, but the use of BOMBLEV -5 makes that conclusion rather speculative. Run the script again with BOMBLEV -1 and note what problems occur; they should be fixed rather than suppressed. If possible, use a CHARMM version compiled for more atoms, e.g. LARGE; that should take care of the NTHETA > MAXT problem.


Rick Venable
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rmv Offline OP
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An additional note-- the READ COOR PDB command has improved since I first developed my approach using READ COOR UNIV; it should be reasonable to use PDB instead of UNIV. The changes needed are:

! ALTERNATE PDB INPUT METHOD; put B-factors in WMAIN
read univ
* modified pdb
*
pdb
segid 22 1
ires 23 4
w 61 6
end


The above section isn't needed, but may be left in place (it is harmless), commented out (via ! char), or deleted. Each READ COOR command is changed from

! PROTEIN FRAGMENT, SEGID A; GET SEQU AND COORDS FROM FILE
open unit 3 read card name irk.pdb
read sequ pdb unit 3
rewind unit 3
gener A setup warn
read coor univ unit 3 offset -980
close unit 3

to

! PROTEIN FRAGMENT, SEGID A; GET SEQU AND COORDS FROM FILE
open unit 3 read card name irk.pdb
read sequ pdb unit 3
rewind unit 3
gener A setup warn
read coor pdb unit 3 offset -980
close unit 3


Rick Venable
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Hi,

I have followed your instructions and used your input file for 1prt with the necessary revisions for my complex, but unfortunately I get always the same warning:

CHARMM> gener c setup warn
THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE
THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE
** WARNING ** BOND NOT FOUND FOR RESIDUE 33 PHE .
ATOMS "N " "HN " WERE REQUESTED.
** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 33 PHE .
ATOMS "N " "-C " "CA " "HN " WERE REQUESTED.
** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 33 PHE .
ATOMS "-C " "N " "CA " "C "
ATOMS "N " "CA " "C " "+N " WERE REQUESTED.
** WARNING ** DONOR NOT FOUND FOR RESIDUE 33 PHE .
ATOMS "HN " "N " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 415 VAL .
ATOMS "C " "+N " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 415 VAL .
ATOMS "O " "C " WERE REQUESTED.
** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 415 VAL .
ATOMS "C " "CA " "+N " "O " WERE REQUESTED.
** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 415 VAL .
ATOMS "-C " "N " "CA " "C "
ATOMS "N " "CA " "C " "+N " WERE REQUESTED.
** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 415 VAL .
ATOMS "O " "C " WERE REQUESTED.

Phe33 and Val415 are the N-term and the C-term, respectively, so I know that some problems have occurred there.
I’m sorry but I tried to change atom names (OT1, OT2 and HN) with no results.
I have all the atoms mentioned in the warning messages in my PDB file, so what can I do?

Any help is really appreciated

Vittorio

P.S. I got the same warning using 1prt.pdb file.


Vittorio Limongelli PhD Student Medicinal Chemistry Faculty of Pharmacy Naples
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rmv Offline OP
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They are just warning messages of the the type usually seen for polymer terminii, and may not be real problems. The real test is can you minimize the structure, or at least evaluate the energy w/o errors.

You may need to check your "necessary revisions" more carefully.

Finally, the example illustrates one way to read only the atoms with existing coords, which was all I needed for a quick look at the subunit contact surfaces. For a more detailed study, one should probably define the residues for the disordered loop in subunit A, and use some model building approaches to define coordinates for these atoms.


Rick Venable
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I’m using your input of 1prt for a complex formed by a DNA molecule and a protein. So I would use the offset option but I have some problems with RESNO.
May you give me some suggestions, or better some script examples, about how I can treat DNA molecule in complex with a protein?

Thanks in advance

Vittorio

Last edited by victor25; 05/18/06 04:04 PM.

Vittorio Limongelli PhD Student Medicinal Chemistry Faculty of Pharmacy Naples
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rmv Offline OP
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Please read the explanatory material at the beginning of this thread, and make sure you completely understand the difference between the RESID and RESNO (a.k.a. IRES). Once you do, how to calculate the needed OFFSET should be clear.


Rick Venable
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I'm sorry, I have just corrected my previous message,
I meant RESNO, not RESID, and I had already read and understood your opening message when I wrote on this topic for the first time, anyway I will try to treat my DNA as a protein subunit in the OFFSET keywork. Is this wrong?
I will communicate any problem on the forum.


Vittorio Limongelli PhD Student Medicinal Chemistry Faculty of Pharmacy Naples
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rmv Offline OP
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Computing the correct OFFSET based on RESID and RESNO has nothing to do with whether the additional segment(s) are nucleic or amino acid based, it depends only on the first RESID in the PDB file, and the next available RESNO for the PSF. Note that the OFFSET can be negative.


Rick Venable
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Hi, I am trying to create first psf file of a pdb complex (protein dimmer plus a ligand). where is the script located?
can you post the link... One more note! how to convert it into psf format.
thanks
s

Last edited by ssn; 07/13/07 11:01 PM.
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