Re: Coarse Grain Angle Parameter Issue

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Sat Jun 18 2016 - 00:23:37 CDT

Hello,

 From a quick glance in the martini-proteins.top file and the section
describing PHE we can see the following:

RESI PHE 0.00 ! - SI2
ATOM BAS P5 0.00 ! | / |
ATOM SI1 SC4f 0.00 ! BAS-SI1 |
ATOM SI2 SC4f 0.00 ! | \ |
ATOM SI3 SC4f 0.00 ! - SI3
BOND BAS SI1 !
BOND SI1 SI2 SI1 SI3 SI2 SI3 !these should be constraints
BOND BAS +BAS !
ANGLE BAS SI1 SI2 !
ANGLE BAS SI1 SI3 !
ANGLE -BAS BAS SI1 !
ANGLE -BAS BAS +BAS !
!other possible ring angles that are not defined in Martini
!these angles should NOT be used
!one should take care to specify "auto none" in psfgen so that it does
not automatically generate them
!the definitions are left here (commented out) as a reminder
!ANGLE SI1 SI2 SI3 ! 60
!ANGLE SI2 SI3 SI1 ! 60
!ANGLE SI3 SI1 SI2 ! 60
IMPR BAS SI2 SI3 SI1
DIHE -BAS BAS +BAS #BAS

As you can see, all angles betweenn side chain particles in ring
structures (i.e. the SI1, SI2 and SI3) are commented out (lines start
with "!") and we are warned to use "auto none" when creating the psf
files with psfgen/autopsf. See, psfgen (and the AutoPSF vmd plugin) can
automatically generate angles not defined in topologies based on
"intuition" (well, geometry,but whatever) and we don't want that in this
case.

You most likely missed that part (it is stated in the tutorial at some
early point). If you used the AutoPSF GUI plugin, search for the option
of "Regenerate Angles/Dihedrals" and disable it, then rebuild your
system. If you used Tcl scripts for psfgen/vmd, then make sure you add
this line so that angles are not automatically generated.

Theoretically, you could try editing the ANGLES section of your psf by
hand and remove all angles (if you don't want to rebuild your system)
but I wouldn't recommend it, since it will probably mess things beyond
recognition. Furthermore, although you don't give the specifics of your
system, I think we can safely assume that all ring structures in your
system (Phe, Tyr, Trp etc) will have the same problem, so editing by
hand is out of the question.

Hope I helped,
Fotis

On 06/18/2016 06:37 AM, Nisler, Collin R. wrote:
>
> Hello, I am attempting to run a coarse grain simulation of a small
> transmembrane protein with a lipid patch. I followed the membrane
> protein and residue based coarse grain tutorials to prepare the
> system, and attempted to run minimization and equilibration using the
> parameter files from the coarse grain tutorial. When I attempted to
> run the simulation, I got the following error:
>
>
> Charm++ fatal error:
>
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR SC4f SC4f SC4f (ATOMS
> 50 52 51)
>
>
> Atoms 50, 51, and 52 are the following in the psf file:
>
>
> 50 AP1 24 PHE SI1 SC4f 0.000000 45.0000 0
> 51 AP1 24 PHE SI2 SC4f 0.000000 45.0000 0
> 52 AP1 24 PHE SI3 SC4f 0.000000 45.0000 0
>
>
> Does anyone have any thoughts on why this is happening? Thanks very
> much for your help.
>
>
> Collin Nisler
>
>

-- 
*******************************************
Fotis A. Baltoumas
Phd Candidate, Bioinformatics Postgraduate Programme
Department of Cell Biology and Biophysics
Faculty of Biology, University of Athens
Panepistimiopolis, Athens 157 01, GREECE
   --------------------------------------
email : fbaltoumas_at_biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
*******************************************

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:33 CST