[gmx-users] Problem with my pull-code or my topology (or both) - help appreciated

[Billy Williams-Noonan]

Hi All,

Just an update.  I regenerated the topology for the linear peptide with the
ATB and found myself with similar problems.

Will this pull until the Z-component of the COM distance is 3.2 nm and hold
it in place?

pull                    = yes

pull_ngroups            = 2
pull_ncoords            = 1
pull_coord1-groups      = 1 2
pull_group1_name        = reference_pull_group
pull_group2_name        = Pull_Group
pull_coord1-type        = umbrella
pull_coord1-geometry    = direction
pull_coord1-dim         = N N Y
;pull_coord1-rate       = 0.00005
pull_coord1-k           = 1000
pull_coord1-vec         = 0 0 1
pull_coord1-init        =  *3.20*
pull_coord1-start       = no

pull_print-components   = yes

pull_nstxout = 10
pull_nstfout = 1

Is this doing what I think it is doing?  Because it has worked for every
other example I have been using.

Best regards,

Billy

On 4 August 2016 at 17:28, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:

> Hi Gromacs Users,
>
> I have been pulling peptides from two separate proteins (let's call them A
> and B) by first taking the crystal structure pose and pulling the ligand to
> progressively more distant points from the binding site, and then sampling
> at that point.
>
> I first pull the ligand out of the binding site over 400ps with a high
> force constant (10000 kJ/mol/nm^2), and then sample at that point with a
> lower force constant (1000 kJ/mol/nm^2)
>
> The pull-code I have been using in my .mdp file is this:
>
> *400 ps Pull*
>
> pull                    = yes
>
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_coord1-groups      = 1 2
> pull_group1_name        = reference_pull_group
> pull_group2_name        = Pull_Group
> pull_coord1-type        = umbrella
> pull_coord1-geometry    = direction
> pull_coord1-dim         = N N Y
> pull_coord1-k           = 20000
> pull_coord1-vec         = 0 0 1
> pull_coord1-init        =* pull-distance  *
> pull_coord1-start       = no
>
> pull_print-components   = yes
>
> pull_nstxout = 10
> pull_nstfout = 1
>
> *20 ns sampling:  *
>
> pull                    = yes
>
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_coord1-groups      = 1 2
> pull_group1_name        = reference_pull_group
> pull_group2_name        = Pull_Group
> pull_coord1-type        = umbrella
> pull_coord1-geometry    = direction
> pull_coord1-dim         = N N Y
> ;pull_coord1-rate       = 0.00005
> pull_coord1-k           = 1000
> pull_coord1-vec         = 0 0 1
> pull_coord1-init        =  *pull-distance*
> pull_coord1-start       = no
>
> pull_print-components   = yes
>
> pull_nstxout = 10
> pull_nstfout = 1
>
> This has worked for two ligands binding to A and one ligand binding to B
> with varying degrees of agreement with experiment.
>
> However, when I try to move my ligands into position with one
> linear-peptide ligand binding to B, the ligand moves to 2.7 nm between the
> two pull-group's COM... and then refuses to move further.  The initial COM
> pull distance was 1.8 nm, and the final pull distance should be 3.2 nm
> between the two pull groups' COM.
>
> A cyclic peptide version of this molecule was pulled from the binding site
> successfully and its topology was generated with the ATB. The linear
> version of this peptide was generated with gmx pdb2gmx and this is the
> *only* difference in the protocol between the two protocols.
>
> So either the pull-code I am using is not doing what I think it is
> (pulling at specific distances along the Z-direction) *OR* the topology
> being generated by *pdb2gmx* is wrong (but I don't think my input is
> defective).  However, this would make sense given I am getting a lot of
> LINCS warnings at some of my positions...
>
> Specifically:
>
>
> *WARNING (1):*
> *lincs-warnangle can not be larger than 90 degrees, setting it to 90.*
>
> Any help would be appreciated... :)
>
> Best regards,
>
> Billy...
>
> --
> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
> <http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
>
>


-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052