[gmx-users] Could not find clayff forcefield
G R
golnaz.chem at gmail.com
Mon Aug 7 09:17:19 CEST 2017
On Sun, Aug 6, 2017 at 3:37 AM, <
gromacs.org_gmx-users-request at 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 <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] question about gmx do_dssp
> Message-ID: <ca0a8739-7c27-0dc8-b7ed-11e18ae42361 at 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
>
> jalemkul at 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 <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Generating topology file for a long polymer
> chain
> Message-ID: <0bccaede-426a-86ab-a739-3e6c14299e76 at 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
>
> jalemkul at 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 <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Gmx hbond
> Message-ID: <f0482039-f9ae-c60b-0265-6388b0286ef5 at 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
>
> jalemkul at 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 <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Could not find clayff forcefield
> Message-ID: <53962137-d0e7-bfd7-5f6f-ba2deefb97d0 at 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
>
> jalemkul at 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 <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] The small organic molecule occurred
> deformation during simulation
> Message-ID: <eb8d65a4-8d3d-6490-834c-ceab92a8c99e at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> --
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