From: sfrickenhaus (Stephan.Frickenhaus_at_awi.de)
Date: Thu Jul 26 2007 - 04:45:13 CDT

Hello,

I have problems with invisible Tube/Trace/Cartoon graphics in VMD 1.8.6
(win32) when my peptide is made cyclic by patching with the PRES LIG1.
Any hint for that?

Also I saw that "solvate" assumes only residues with name TIP3.
solvate for non-standard should have an argument for non-standard resnames.
Also the segment name "QQQ" is not a flexible thing. I made my copy of
solvate.tcl and made changes therein.

In autopsf-gui I saw that a LIG-patch must be specified last-first, i.e.,
the first residue in the GUI-patch-editor must be the last of my chain
and the second (the "optional one") must be the first of the chain.

I have the impression that the measure-gofr cannot filter for only
displaying non-bonded distances.
How can I make a selection1 selection2 that excludes bonds between sel1
and sel2?
Any way to modify the gofr.tcl for that?

Any suggestions for building a DMSO-Box?
I did it from the dmso.gro from Gromacs-Distribution and made it with
explicit hydrogens due to Feller and Strader JPC(A) 2002
with the following 2 files:
dmso.par:
! parameters by Feller and Strader JPCa 2002
BONDS
CCD SSD 240 1.8
CCD HHD 322 1.11
SSD OOD 540 1.53

ANGLES
HHD CCD HHD 35.5 108.4
HHD CCD SSD 46.1 111.3
CCD SSD OOD 79.0 106.75
CCD SSD CCD 34.0 95.0

DIHEDRALS
HHD CCD SSD OOD 0.2 3 0
HHD CCD SSD CCD 0.2 3 0

NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5

HHD 0.0 -0.024 1.34
CCD 0.0 -0.078 2.04
SSD 0.0 -0.350 2.00
OOD 0.0 -0.120 1.70

HBOND CUTHB 0.5
END

dmso.top:
MASS 294 OOD 15.9994
MASS 295 SSD 32.06
MASS 296 CCD 12.011
MASS 297 HHD 1.008

DECL -CA
DECL -C
DECL -O
DECL +N
DECL +HN
DECL +CA
DEFA FIRS NONE LAST N
AUTO ANGLES DIHE

RESI DMSO 0.0
GROUP
ATOM CD1 CCD -0.1
ATOM CD2 CCD -0.1
ATOM H1 HHD 0.09
ATOM H2 HHD 0.09
ATOM H3 HHD 0.09
ATOM H4 HHD 0.09
ATOM H5 HHD 0.09
ATOM H6 HHD 0.09
ATOM SD SSD 0.312
ATOM OD OOD -0.556
BOND CD1 H1 CD1 H2 C
BOND CD2 H4 CD2 H5 C
BOND SD CD1 SD CD2
!DOUBLE SD OD
ACCEPTOR OD SD

When having the DOUBLE SD OD, my psf really gets 2 Bonds. Is this a
feature or a bug?

Best regards,
Stephan

PS: who wants to try the box, ask me for psf and pdb.

-- 
Prof. Dr. Stephan Frickenhaus
 Alfred-Wegener-Institut f. Polar- u. Meeresforschung
 Am Handelshafen 12
 27570 Bremerhaven
 stephan.frickenhaus_at_awi.de
 0471-4831-1179
 0151-1741 1631
 Hochschule Bremerhaven - Bio-Analytik, FB 1
 An der Karlstadt 8
 27568 Bremerhaven
 0471-4823-525
 0151-1741 1631