On Sun, Aug 6, 2017 at 3:37 AM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. Re: question about gmx do_dssp (Justin Lemkul)
>    2. Re: Generating topology file for a long polymer chain
>       (Justin Lemkul)
>    3. Re: Gmx hbond (Justin Lemkul)
>    4. Re: Could not find clayff forcefield (Justin Lemkul)
>    5. Re: The small organic molecule occurred deformation during
>       simulation (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 5 Aug 2017 20:33:32 -0400
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] question about gmx do_dssp
> Message-ID: <ca0a8739-7c27-0dc8-b7ed-11e18ae42...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/5/17 8:12 PM, Mark Abraham wrote:
> > Hi,
> >
> > I'd start by checking if that last residue is a normal one...
> >
>
> The check_oo() function in gmx_do_dssp.cpp looks like it will not work
> correclty
> for CHARMM, because it does not identify CHARMM termini, thereby ignoring
> the
> C-terminus.  It looks for O, O1, or OC1 (which actually doesn't appear to
> be
> used by any force field).  CHARMM uses OT1/OT2 for COO- termini, so a
> check for
> OT1 needs to be added.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 5 Aug 2017 20:34:59 -0400
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Generating topology file for a long polymer
>         chain
> Message-ID: <0bccaede-426a-86ab-a739-3e6c14299...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/5/17 8:12 AM, Mahsa E wrote:
> > Dear gmx-users,
> >
> > I am trying to build a polymer box from scratch and generate the required
> > input files. So far, I did these steps:
> > 1. built a chain of the polymer
> > 2. run ACPYPE to generate the topology file...
> > However, since the chain is long, it took so long time with ACPYPE and
> the
> > calculation is timed out without convergence.
> >
> > - Is it possible to restart the ACPYPE calculation?
> >
> > I read in some tutorials that it is also possible to run the ACPYPE
> > calculations for the monomeric unit instead and repeat its parameters for
> > the whole chain. How is it possible? The polymer chain may have a
> > conformation with different angles and dihedrals than in the monomer.
> > In general, how can I use the topology file of a monomer for the longer
> > chain of a polymer ?
> > Could you please advise me?
> >
>
> You parametrize the monomer (charges, atom types, bonded parameters), then
> build
> up by doing, e.g. conformational energy scans of dihedral rotations
> between the
> dimer.  That way you can build a proper model of the whole polymer.  Do
> not try
> to parametrize an entire polymer at once; you'll end up with a
> conformation-specific solution for a given geometry, if you can even get
> it to
> work at all.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 5 Aug 2017 20:35:56 -0400
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Gmx hbond
> Message-ID: <f0482039-f9ae-c60b-0265-6388b0286...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/4/17 11:13 AM, farial tavakoli wrote:
> >   blockquote, div.yahoo_quoted { margin-left: 0 !important;
> border-left:1px #715FFA solid !important; padding-left:1ex !important;
> background-color:white !important; }  Dear gromacs user
> > I am performing protein ligand complex (t4lysosim) and now i need to
> analyze JZ4 hydrogen bonding, but when i type Gmx hbondThere is no JZ4 in
> the list to choose. It is because of i used :Gmx make_ndx -f em.gro -o
> index.ndxAnd merged the " protein " and " JZ4" groupsIs there anyone help
> me how to check the hydrogen bond of JZ4 ligand?
>
> Both protein and ligand are default groups and do not require the use of an
> index file.  If the ligand isn't showing up in the list, it's probably
> because
> you're supplying an index file from which the ligand group has been
> deleted.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 5 Aug 2017 20:36:21 -0400
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Could not find clayff forcefield
> Message-ID: <53962137-d0e7-bfd7-5f6f-ba2deefb9...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/4/17 4:57 AM, G R wrote:
> > Dear users,
> >
> > I try to implement Clayff forcefield for Kaolinite. I created my force
> > field (I'm not sure about it), but gromacs couldn't find my force field
> in
> > the directory. Here is my forcefield.
> >
> > ffnonbonded
> > [ atomtypes ]
> > ; name       mass      charge    ptype      sigma      eps
> >   HW   1      1.00800     0.4100    A    0.00000e-01  0.00000e-01
> > ;clayFF_waterhydrogen
> >   HO   1      1.00800     0.4250    A    0.00000e-01  0.00000e-01
> > ;clayFF_hydroxylhydrogen
> >   OW   8     15.99800    -0.8200    A    3.16557e-01  6.50209e-01
> > ;ClayFF_wateroxygen
> >   OH   8     15.99800    -0.9500    A    3.16557e-01  6.50209e-01
> > ;ClayFF_hydroxyloxygen
> >   OB   8     15.99800    -1.0500    A    3.16557e-01  6.50209e-01
> > ;ClayFF_bridgingoxygen
> >   OBOS 8     15.99800    -1.1808    A    3.16557e-01  6.50209e-01
> > ;ClayFF_bridgingoxygenoctasub
> >   OBTS 8     15.99800    -1.1688    A    3.16557e-01  6.50209e-01
> > ;ClayFF_bridgingoxygentetrsub
> >   OHS  8     15.99800    -1.0808    A    3.16557e-01  6.50209e-01
> > ;ClayFF_hydroxyloxygensub
> >   SI  14     28.08600     2.1000    A    3.30208e-01  8.0e-06
> > ;ClayFF_tetrahedralsilicon
> >   AO  13     26.98200     1.5750    A    4.27128e-01  6.0e-06
> > ;ClayFF_octahedalaluminium
> >   AT  13     26.98200     1.5750    A    3.30206e-01  8.0e-06
> > ;ClayFF_tetrasubaluminium
> >
> > ffbonded
> > [ bondtypes ]
> > ; i    j  func       b0          kb
> >   OW     HW   1        0.1000     554134.9
> >   OH     HO   1        0.1000     554134.9
> >   OHS    HO   1        0.1000     554134.9
> >
> > [ angletypes ]
> > ;  i    j    k  func       th0       cth
> >   HW   OW    HW    1        109.47    191.5000064
> >   AL   OH    HO    1        109.47    125.52
> >
> > atomtype.n2t
> > H    HW    0.4100     1.008  1    O  0.100             ;water hydrogen
> > O    OW   -0.8200    15.998  2    H  0.100    H  0.100 ;water oxygen
> > OH2  OH   -0.9500    15.998  1    H  0.100             ;hydroxyl oxygen
> > O2   obts  -1.1688  15.998  0                        ;bridging oxygen
> with
> > tetrahedral substitution
> > O1   obss  -1.2996  15.998  0                     ;bridging oxygen with
> > double substitution
> > OH1  ohs   -1.0808   15.998  1      H  0.100       ;hydroxyl hydrogen
> with
> > substitution
> > Si   st    2.1000    28.086  0                     ;tetrahedral silicon
> > Al   ao    1.5750    26.982  0                     ;octahedral aluminium
> > Mg  mgo    1.3600    24.305  0                     ; octahedral magnisium
> > Na   Na    1.0000    22.999  0                     ;sodium ion
> >
> > forcefield.doc
> > clayff.ff force field
> >
> > forcefield.itp
> > #define _ff_clayff
> >
> >
> > [ defaults ]
> >   ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> >   1               3               yes             0.5     0.5
> >
> > #include "ffnonbonded.itp"
> > #include "ffbonded.itp"
> >
> > pdb
> >
> > Al    0.649    4.333    3.377
> > Al    3.24    8.805    3.377
> > Al    3.203    2.851    3.362
> > Al    0.639    7.324    3.362
> > Si    4.962    3.016    0.65
> > Si    2.398    7.488    0.65
> > Si    2.442    1.47    0.653
> > Si    -0.122    5.942    0.653
> > O1    -0.334    3.098    2.268
> > O1    2.258    7.57    2.268
> > O1    0.041    5.839    2.271
> > O1    2.605    1.367    2.271
> > O3    0.014    4.472    0
> > O3    -1.885    4.259    7.154
> > O3    5.169    4.472    0
> > O3    3.27    4.259    7.154
> > O3    2.578    0    0
> > O3    0.678    -0.214    7.154
> > O3    2.605    8.945    0
> > O3    0.706    8.731    7.154
> > O3    1.034    2.056    0.177
> > O3    3.626    6.529    0.177
> > O3    1.052    6.848    0.023
> > O3    3.616    2.376    0.023
> > OH1    -0.322    8.606    2.304
> > OH1    2.242    4.133    2.304
> > OH2    3.83    1.36    4.329
> > OH2    1.266    5.832    4.329
> > OH2    -0.962    4.136    4.35
> > OH2    1.629    8.608    4.35
> > OH2    -0.961    7.535    4.36
> > OH2    1.602    3.063    4.36
> > O2    2.633    10.312    2.271
> > OH2    3.858    10.305    4.329
> > OH2    4.834    8.606    2.304
> > OH2    4.194    7.535    4.36
> > O3    4.821    3.098    2.268
> > OH3    4.193    4.136    4.35
> > O3    6.19    2.056    0.177
> > O3    -1.529    6.529    0.177
> >
> >
> > It's to long, Sorry about it, but I really need to find out where is my
> > problem. I put n2t file in directory not in my forcefield subdirectory.
> Do
>
> That's wrong.  It needs to be in the force field subdirectory.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
    Thank you Justin, I changed it to subdirectory, but still doesn't work.
Would you please take a   quick look on the files? Are these files that I
copied here enough to create bonds?


>
> ------------------------------
>
> Message: 5
> Date: Sat, 5 Aug 2017 20:37:16 -0400
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] The small organic molecule occurred
>         deformation during simulation
> Message-ID: <eb8d65a4-8d3d-6490-834c-ceab92a8c...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/4/17 4:42 AM, yujie liu wrote:
> >
> > Hello, users
> >
> > I?m a novice to study the gromacs program. Now I met some problems which
> the small molecule occurred deformation when energy minimization was
> performed. For example, the anthracene molecule became bent in the plane of
> C-rings, the same as phenol. I want to know whether  the situation is
> normal? In addition, I employed gromos54a7.ff
> >
>
> Slight out-of-plane distortions are possible because the rings aren't fully
> rigid.  But if you're seeing significant distortion, it suggests your
> topology
> is wrong, likely due to missing or incorrect improper dihedrals, which
> serve to
> prevent out-of-plane deformation.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> --
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