[gmx-users] Engergy minimization

[David]

On Tue, 2005-09-13 at 15:59 +0100, Naser, Md Abu wrote:
> Hi All,
> 
> I have a bad starting structure with an atom having infinite max
> force. I tried moving the atom manually as Eric suggested  and stuck
> in local minima. Erick also sggested using soft-core potential. I have
> been wondering  whether I can do it with gromacs. I dont want to do
> free energy calculation. I just want to minimize the energy using
> soft-core potential.
Just check mdp option on the website.
> 
> With regards,
> Abu
> 
> PhD Student
> School Of Life Sciences
> Heriot-Watt University
> Edinburgh
> EH14 4AS
> Phone: +44(0)1314518265
> 
> 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org on behalf of Erik Lindahl
> Sent: Wed 9/7/2005 12:26 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Engergy minimization
> 
> Nope, theoretically impossible.
> 
> You'll have to start by getting get rid of the inifinite force. Move 
> the atoms manually, or use soft-core interactions.
> 
> Cheers,
> 
> Erik
> 
> 
> 
> On Sep 7, 2005, at 1:02 PM, Naser, Md Abu wrote:
> 
> > Hi All,
> >
> >
> >
> > I have an atom with infinite maximum force in a protein. Is any 
> > protocol of energy minimization that can handle this situation?
> >
> > With regards,
> > abu
> >
> >
> >
> >
> >
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org on behalf of Naser, Md Abu
> > Sent: Tue 9/6/2005 11:13 AM
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] Segmentation fault
> >
> > Hi All,
> >
> > I have included a new amino acid- phosphoserine(PSE) in rtp file. 
> > Although,I  included the amino acid in ffG43a1.hdb and
> >
> > pdb2gmx -f xxx.pdb -o xxx.gro -ignh -missing -p xxx.top, gives
> >
> > WARNING: atom H is missing in residue PSE 67 in the pdb file
> >          You might need to add atom H to the hydrogen database of 
> > residue PSE
> >          in the file ff???.hdb
> >
> > When I run mdrun, i am getting segmentation fault.
> >
> >
> > Can anyone advise me where might be problem?
> >
> >
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > ~~~~~~~~
> >  in ffG43a1.rtp
> > [ PSE ]
> >
> >  [ atoms ]
> >     N     N    -0.28000     0
> >     H     H     0.28000     0
> >    CA   CH1     0.00000     1
> >    CB   CH2     0.15000     2
> >    OG    OA    -0.54800     2
> >    P     P      0.79800     2
> >    O1P   OM    -0.80000     2
> >    O2P   OM    -0.80000     2
> >    O3P   OM    -0.80000     2
> >     C     C       0.380     3
> >     O     O      -0.380     3
> >  [ bonds ]
> >     N     H    gb_2
> >     N    CA    gb_20
> >    CA     C    gb_26
> >     C     O    gb_4
> >     C    +N    gb_9
> >    CA    CB    gb_26
> >    CB    OG    gb_17
> >     P    O1P   ga_23
> >     P    O2P   ga_23
> >     P    O3P   ga_23
> >     P    OG    ga_27
> >  [ angles ]
> > ;  ai    aj    ak   gromos type
> >    -C     N     H     ga_31
> >     H     N    CA     ga_17
> >    -C     N    CA     ga_30
> >     N    CA     C     ga_12
> >    CA     C    +N     ga_18
> >    CA     C     O     ga_29
> >     O     C    +N     ga_32
> >     N    CA    CB     ga_12
> >     C    CA    CB     ga_12
> >    CA    CB    OG     ga_12
> >    OG     P    O1P    ga_23
> >    OG     P    O2P    ga_23
> >    OG     P    O3P    ga_23
> >    CB    OG     P     ga_27
> >    O1P    P    O2P    ga_28
> >    O1P    P    O3P    ga_28
> >    O2P    P    O3P    ga_28
> >  [ impropers ]
> > ;  ai    aj    ak    al   gromos type
> >     N    -C    CA     H     gi_1
> >     C    CA    +N     O     gi_1
> >    CA     N     C    CB     gi_2
> >  [ dihedrals ]
> > ;  ai    aj    ak    al   gromos type
> >   -CA    -C     N    CA     gd_4
> >    -C     N    CA     C     gd_19
> >     N    CA     C    +N     gd_20
> >     N    CA    CB    OG     gd_17
> >    CA    CB    OG     P     gd_12
> >    CB    OG     P   O1P     gd_11
> >    CB    OG     P   O2P     gd_11
> >    CB    OG     P   O3P     gd_11
> >
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > ~~~~~~~~~~~~~~~~~~~~~~~~
> > in ffG43a1.hdb
> > PSE     2
> >         1       1       N       -C      CA
> >         1       2       OG       CB     CA
> >
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >
> >
> >
> >
> > _______________________________________________
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> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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