[gmx-users] Engergy minimization

[Naser, Md Abu]

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.

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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