Re: Help! There is no angle or dihedral definitions for patches in .psf!

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Apr 29 2004 - 13:23:55 CDT

What happens if you just leave out the first and last directives in your
psfgen script?

Brian

On Thu, 29 Apr 2004, Edward Patrick Obrien wrote:

>
> I tried sending this message yesterday but it appears it didn't go
> through...
>
> On Wed, 28 Apr 2004, Ed wrote:
>
> Hi All,
> Serious problem here (I think), I create a .pdb and .psf with patches
> of CT3 (methyl amide) and ACE, but in the .psf file there is no angle
> definitions nor dihedral definitions for the patched atoms!
>
> This leads to serious problems... when I minimize, or run MD, the atoms
> in the patches contort and float around like they don't feel each other,
> outrageous bond angles can occur! And finally the system crashes at some
> point because RATTLE can't take it.
>
> Why are angle and dihedral not being defined? How can I correct it?
>
> Just in case you don't believe me check this out:
>
> If I just use the Standard NTER and CTER in charmm (less atoms then ACE
> and CT3) the number of angles and dihedrals are:
>
> Info: writing psf file test.psf
> total of 172 atoms
> total of 174 bonds
> total of 314 angles
> total of 461 dihedrals
> total of 21 impropers
>
> Now if I patch with CT3 and ACE:
>
> Info: writing psf file test.psf
> total of 181 atoms
> total of 183 bonds
> total of 307 angles
> total of 453 dihedrals
> total of 24 impropers
>
> So there are more Atoms but less angles and dihedrals? Sounds crazy to
> me.
>
> Also here are the positions of the hydrogens on the carbon of the
> amide-methyl BEFORE minimization:
>
> ATOM 170 HT1 SER 11 19.167 -0.569 0.788 1.00 0.00
> ATOM 171 HT2 SER 11 19.311 -2.153 1.177 1.00 0.00
> ATOM 172 HT3 SER 11 20.181 -1.533 -0.064 1.00 0.00
>
> Here are the same hydrogens AFTER 2000 steps of minimization:
>
> ATOM 170 HT1 SER 11 20.509 -1.046 0.825 1.00 0.00
> ATOM 171 HT2 SER 11 20.560 -1.180 0.961 1.00 0.00
> ATOM 172 HT3 SER 11 20.432 -1.047 0.906 1.00 0.00
>
> Notice anything strange!? The atoms are practically on top of each
> other!?
>
> Here is the TCL script I use to create the .pdb and .psf:
>
> package require psfgen
> topology top_all27_prot_lipid.inp
> segment X {
> first none
> last none
> pdb X_start.pdb}
> patch ACE X:1
> patch CT3 X:11
> coordpdb X_start.pdb X
> guesscoord
> writepdb test.pdb
> writepsf test.psf
>
> Any suggestions would be much appreciated,
> Ed
>
> PS - I've tried using 'auto' to no avail.
> >
> >
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************

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