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#11592 - 08/23/06 04:39 AM How to deal with expanded format??
accelrys Offline
Forum Member

Registered: 06/21/06
Posts: 21
I have some of the output file below:
CHARMM> ! put the complex in a water box
CHARMM> read sequ tip3 21173

CHARMM> gene wat1 noangle nodihe
NO PATCHING WILL BE DONE ON THE FIRST RESIDUE
NO PATCHING WILL BE DONE ON THE LAST RESIDUE
GENPSF> Segment 2 has been generated. Its identifier is WAT1.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 2 Number of residues = 21745
Number of atoms = 72299 Number of groups = 23862
Number of bonds = 72427 Number of angles = 37194
Number of dihedrals = 23549 Number of impropers = 1535
Number of cross-terms = 570
Number of HB acceptors = 22035 Number of HB donors = 973
Number of NB exclusions = 0 Total charge = -17.00000
QXFORM> Expanded format used.
More than 4 character RESID used.

I wonder how to deal with it.Thanks!

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#11593 - 08/23/06 04:56 AM Re: How to deal with expanded format?? [Re: accelrys]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4742
Loc: ~ 59N, 15E
This is just an informative message, and no error condition. You don't have to deal with it; CHARMM deals with it for you.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#11594 - 08/23/06 08:45 PM Re: How to deal with expanded format?? [Re: lennart]
accelrys Offline
Forum Member

Registered: 06/21/06
Posts: 21
Thanks,professor. But my crd file which produced together with this output file has many errors read by VMD as following.
error> Base molecule :Excessive bonding errors encountered,perhaps atom coodinates are in the wrong units?
error> Base molecule :Silencing bonding error messeges.
<warning> Unusual bond between residues: 3 <protein> and 11251 <water>
.
.
.

I am sure that my initial model before putting into the water box is minimized without error.
I do not know what caused this.

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#11595 - 08/23/06 09:44 PM Re: How to deal with expanded format?? [Re: accelrys]
rmv Offline

Forum Member

Registered: 09/17/03
Posts: 8379
Loc: 39 03 48 N, 77 06 54 W
If CHARMM can re-read the file, then it may be a VMD error; only newer versions of VMD can read the CHARMM expanded format coord files, and a "plug-in" may be needed.
_________________________
Rick Venable
computational chemist


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