[gmx-users] Archaeal lipid packages for Gromos 53A6
Wainwright, Josh
joshua.wainwright.11 at ucl.ac.uk
Tue Aug 12 17:46:26 CEST 2014
Thanks again Justin. I will try to run archaeal lipids with CHARMM36.
Josh
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Today's Topics:
1. Re: gromacs.org_gmx-users Digest, Vol 124, Issue 55
(Wainwright, Josh)
2. Re: Archaeal lipid packages for Gromos 53A6 (Justin Lemkul)
3. Iron containing structure simulation crash (Nikolaos Michelarakis)
----------------------------------------------------------------------
Message: 1
Date: Tue, 12 Aug 2014 15:08:38 +0000
From: "Wainwright, Josh" <joshua.wainwright.11 at ucl.ac.uk>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 124, Issue
55
Message-ID: <1407856118370.24346 at ucl.ac.uk>
Content-Type: text/plain; charset="iso-8859-1"
Thanks for the prompt response Justin. We are working with protein fragments with between 1 and 3 helices.
I've noticed that Anirban Ghosh made a tutorial based on yours, and he used Gromos43a1 for a GPCR (7 helices) in bacterial membranes (POPC in his case, as opposed to DPPC in your case with the model KALP-15 protein). Do you think 43a1 is a good alternative, or is there any other forcefield you would recommend?
I've also seen people recommend CHARMM36.
Thank you!
Josh
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Today's Topics:
1. Re: Protein-ligand complex energy minimization (Justin Lemkul)
2. Re: Problem in Ligand-Protein complex in POPC (Justin Lemkul)
3. Re: AVX vs AVX2 (Szil?rd P?ll)
4. Re: Archaeal lipid packages for Gromos 53A6 (Wainwright, Josh)
5. Re: Archaeal lipid packages for Gromos 53A6 (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Tue, 12 Aug 2014 07:38:08 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Protein-ligand complex energy minimization
Message-ID: <53E9FCA0.7040406 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 8/12/14, 4:58 AM, Indu Kumari wrote:
> Grompp terminated and shows following warning and notes:
> NOTE 1 [file topol.top, line 57]:
> System has non-zero total charge: -0.675997
> Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> for discussion on how close it should be to an integer.
>
Your topology is badly broken.
>
>
> Warning: atom name 3706 in topol.top and fws_ion.pdb does not match (O1 -
> OW)
> Warning: atom name 3707 in topol.top and fws_ion.pdb does not match (P1 -
> HW1)
> Warning: atom name 3708 in topol.top and fws_ion.pdb does not match (O2 -
> HW2)
> Warning: atom name 3709 in topol.top and fws_ion.pdb does not match (O3 -
> OW)
> Warning: atom name 3710 in topol.top and fws_ion.pdb does not match (O -
> HW1)
> Warning: atom name 3711 in topol.top and fws_ion.pdb does not match (P2 -
> HW2)
> Warning: atom name 3712 in topol.top and fws_ion.pdb does not match (O5 -
> OW)
> Warning: atom name 3713 in topol.top and fws_ion.pdb does not match (O6 -
> HW1)
> Warning: atom name 3714 in topol.top and fws_ion.pdb does not match (O4 -
> HW2)
> Warning: atom name 3715 in topol.top and fws_ion.pdb does not match (NA -
> OW)
> Warning: atom name 3716 in topol.top and fws_ion.pdb does not match (NA -
> HW1)
> Warning: atom name 3717 in topol.top and fws_ion.pdb does not match (NA -
> HW2)
> Warning: atom name 3718 in topol.top and fws_ion.pdb does not match (NA -
> OW)
> Warning: atom name 3719 in topol.top and fws_ion.pdb does not match (NA -
> HW1)
> Warning: atom name 3720 in topol.top and fws_ion.pdb does not match (NA -
> HW2)
> Warning: atom name 3721 in topol.top and fws_ion.pdb does not match (NA -
> OW)
> Warning: atom name 3722 in topol.top and fws_ion.pdb does not match (NA -
> HW1)
> Warning: atom name 3723 in topol.top and fws_ion.pdb does not match (NA -
> HW2)
> Warning: atom name 3724 in topol.top and fws_ion.pdb does not match (NA -
> OW)
> Warning: atom name 3725 in topol.top and fws_ion.pdb does not match (NA -
> HW1)
> (more than 20 non-matching atom names)
>
> WARNING 1 [file topol.top, line 57]:
> 43 non-matching atom names
> atom names from topol.top will be used
> atom names from fws_ion.pdb will be ignored
>
The topology is also out of order with respect to the coordinate file, so any
simulation that uses it will be totally nonsensical. The order of [molecules]
must exactly match that of the coordinate file, though given the nasty charge
shown above, you have probably broken something else much earlier.
>
> Analysing residue names:
> There are: 350 Protein residues
> There are: 4 Other residues
> There are: 15 Ion residues
> There are: 21556 Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 205188.00
> Largest charge group radii for Van der Waals: 6.365, 3.730 nm
> Largest charge group radii for Coulomb: 6.365, 4.811 nm
>
> WARNING 2 [file em.mdp]:
> The sum of the two largest charge group radii (11.176151) is larger than
> rlist (1.000000)
>
This is either the result of having broken some molecule(s) incorrectly or may
simply be due to PME. Given the large charge group radii shown, I suspect the
former.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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: Tue, 12 Aug 2014 07:42:01 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Problem in Ligand-Protein complex in POPC
Message-ID: <53E9FD89.1000806 at vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
On 8/12/14, 6:50 AM, neha bharti wrote:
> Thank you very much justin for your reply.
>
> But I am still facing the problem to include ligand in protein.
>
> Following step I am performing:
>
>
> PDB file of protein complex with ligand is taken from pdb
> then
>
> 1) editconf -princ -f protein.pdb -o protein_princ.pdb
>
> 2) editconf -rotate 0 0 90 -f protein_princ.pdb -o protein_princ_rotate.pdb
>
>
> 3) separate protein and ligand files from protein_princ_rotate and then save
> then in different files
>
> protein file: protein_princ_rotate.pdb
>
> ligand file: lig_princ_rotate.pdb
>
>
>
> 4) generating pdb and itp file for small molecule
> lig.pdb
> lig.itp
>
Are the coordinates of lig.pdb identical to those of lig_princ_rotate.pdb?
>
> 5) Generation of topology files for protein:
>
> pdb2gmx -f protein_princ_rotate.pdb -water tip3p -ignh -o protein.pdb
> -nochargegrp
>
>
> 6) mearge protein.pdb and lig.pdb file in conf.pdb file
>
>
> 7) copy the files (mention in tutorial) from charmm36 force field and place
> them in new created folder charmm36_lipid.ff
>
>
> 8) Next, create a forcefield.doc file that contains a description of the
> force field parameters in it. Mine contains something like:
>
> CHARMM36 all-atom lipid force field (with CMAP), extended to include Berger
> lipid parameters
>
Don't do this! CHARMM36 and Berger are incompatible. CHARMM36 already includes
the lipid force field.
>
> 9) changes in topology file "charmm36/tip3p.itp" to
> "charmm36_lipid.ff/tip3p.itp"
>
>
> 10) Add Ligand Topology file:
>
> ; Include ligand topology
> #include "lig.itp"
>
> ; Include water topology
> #include "charmm36.ff/spc.itp"
>
Don't use SPC. It will re-define the water [moleculetype] and apply the wrong
parameters. Make sure you're using the CHARMM-specific TIP3P model (default in
the charmm36.ff package we provide). If you don't, the lipid force field will
produce bad results.
> 11) The next adjustment to be made is in the [ molecules ] directive. To
> account for the fact that there is a new molecule in conf.gro, we have to
> add it here, like so:
>
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> LIG 1
>
> download the following files:
>
> popc128a.pdb - the structure of a 128-lipid POPC bilayer
> popc.itp - the moleculetype definition POPC
> lipid.itp - Berger lipid parameters
>
You need an all-atom model of the lipid bilayer. CHARMM-GUI is a better source
of these coordinates. Don't use the united-atom Berger model from Peter
Tieleman in this case.
>
> 12) Orient the protein and membrane
>
> Convert the popc128.pdb to .gro format with editconf and remove the initial
> periodicity.
>
> (a) Generate a .tpr file for a popc-only system using grompp.
>
> grompp -f em.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr
>
>
> (b) Use trjconv to remove periodicity:
>
> trjconv -s em.tpr -f popc128a.pdb -o popc_whole.gro -pbc mol -ur compact
>
> select 0 for system
>
>
> 13) orient the peptide within this same coordinate frame as lipid, and place
> the center of mass of the peptide at the center of this box:
>
> editconf -f conf.gro -o conf_newbox.gro -c -box 6.23910 6.17970 6.91950
>
>
> 14) Pack the lipids around the protein and ligand complex
>
> First, concatenate the protein and bilayer structure files:
>
> cat conf_newbox.gro popc_whole.gro > system.gro
>
>
> 15) Remove unnecessary lines
>
> 16) Now, generate this new position restraint file using genrestr and
> include it in topology file:
>
> genrestr -f conf_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
>
> select 0 for system
>
> 17)In the .mdp file used for the minimizations, add a line "define =
> -DSTRONG_POSRES" to make use of these new position restraints.
>
>
> 18) seperate the ligand and protein file because InflateGRO not deal with
> small molecule.
>
> then InflateGRO script run:
>
> perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat
>
> 19) energy minimize:
>
> grompp -f em.mdp -c system_inflated.gro -p topol.top -o em.tpr
>
> mdrun -v -deffnm em
>
> another script command:
>
> perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat
>
> Another energy minimization step:
>
> grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr
>
> mdrun -v -deffnm em
> Repeat this step.
>
> area per lipid reached ~69 ? square. Then I stop.
>
> then again include the small molecule to final system_shrink.gro file and
> after that I perform the steps that is given in tutorial.
>
>
>
> is this the right way. I am doing this because we have to show the
> interaction of ligand and protein. I first created the ligand protein
> complex and at the time of running inflategro.pl command I separate the
> ligand molecule and again include it after iterations of scaling down by
> 0.95.
>
In principle, yes - the ligand should be removed before running InflateGRO, then
added once the system is properly compressed. Have you detected some problem at
this point?
> rest of the steps is same as given in tutorial.
>
>
>
> one more query can we use orientation of protein in membrane database
> http://opm.phar.umich.edu/
> for orientation of protein instead of editconf???
> as it is not giving me the correct alignment.
>
Never used it, so I can't comment.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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: Tue, 12 Aug 2014 15:11:47 +0200
From: Szil?rd P?ll <pall.szilard at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>, Pappu
Kumar <papuu_k at yahoo.com>
Subject: Re: [gmx-users] AVX vs AVX2
Message-ID:
<CANnYEw5vQouwaCokRySrXXsiTWV4uKfBu6gwUEx-2NrtH0CoEA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Yes, it definitely will. The difference will be quite pronounced in
CPU-only runs, but if you use a GPU this will shrink and could become
relatively small depending on the turbo/frequency scaling settings
you'll use.
--
Szil?rd
On Tue, Aug 12, 2014 at 9:37 AM, Pappu Kumar <papuu_k at yahoo.com> wrote:
> I am planning to buy an Intel Haswell-E 5820 processor which supports AVX2. I am wondering if it will have better performance than i7 4930K which supports AVX. Thank you.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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------------------------------
Message: 4
Date: Tue, 12 Aug 2014 14:52:47 +0000
From: "Wainwright, Josh" <joshua.wainwright.11 at ucl.ac.uk>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Archaeal lipid packages for Gromos 53A6
Message-ID: <1407855166656.51653 at ucl.ac.uk>
Content-Type: text/plain; charset="iso-8859-1"
Hello everybody,
I am trying to find some archaeal lipid packages to work in Gromss 53A6 forcefield and have only come across those on the website lipid book:
http://lipidbook.bioch.ox.ac.uk/package/show/id/20.html
Unfortunately these lipid parameters are not working quite as we expected and give a very large RMSD for our protein in the system which we believe the lipid parameters are to blame.
If anyone has any other archaeal lipid packages or knows where to find them help would be gratefully appreciated.
Regards,
Joshua Wainwright?
------------------------------
Message: 5
Date: Tue, 12 Aug 2014 10:55:03 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Archaeal lipid packages for Gromos 53A6
Message-ID: <53EA2AC7.80008 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 8/12/14, 10:52 AM, Wainwright, Josh wrote:
> Hello everybody,
>
> I am trying to find some archaeal lipid packages to work in Gromss 53A6 forcefield and have only come across those on the website lipid book:
>
> http://lipidbook.bioch.ox.ac.uk/package/show/id/20.html
>
> Unfortunately these lipid parameters are not working quite as we expected and give a very large RMSD for our protein in the system which we believe the lipid parameters are to blame.
>
Does the protein have a high helical content? If so, then it's the 53A6 protein
parameters that are to blame; that force field is known to understabilize
helices, in some cases dramatically.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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------------------------------
Message: 2
Date: Tue, 12 Aug 2014 11:12:23 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Archaeal lipid packages for Gromos 53A6
Message-ID: <53EA2ED7.1090503 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 8/12/14, 11:08 AM, Wainwright, Josh wrote:
> Thanks for the prompt response Justin. We are working with protein fragments with between 1 and 3 helices.
>
> I've noticed that Anirban Ghosh made a tutorial based on yours, and he used Gromos43a1 for a GPCR (7 helices) in bacterial membranes (POPC in his case, as opposed to DPPC in your case with the model KALP-15 protein). Do you think 43a1 is a good alternative, or is there any other forcefield you would recommend?
>
43A1 or 54A7 would probably be better.
> I've also seen people recommend CHARMM36.
>
CHARMM36 has excellent lipid parameters, better than Berger for most observables.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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: Tue, 12 Aug 2014 16:19:32 +0100
From: Nikolaos Michelarakis <nm884 at york.ac.uk>
To: gmx-users at gromacs.org
Subject: [gmx-users] Iron containing structure simulation crash
Message-ID:
<CADp34c=uOiiFgr8XsfV+=UTK9ZArwsZEHM7vS-rSvCCs_a89vw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hello again,
I finally managed to introduce the iron into my structure and generate a
topology. However, when i first run the initial energy minimization, either
in vacuum or with solvent, i get the following message:
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, but this is often
notneeded for preparing to run molecular dynamics.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 36 steps,
but did not reach the requested Fmax < 500.
Potential Energy = -4.2946888e+05
Maximum force = 6.7161971e+08 on atom 2832
Norm of force = 1.7847602e+07
however, a .gro file is produced. When I try to run the next step with this
.gro file I get a bunch of LINCS warnings and after a few steps the
simulation crashes with this message:
/opt/gridengine/default/spool/compute-0-5/job_scripts/11107: line 15: 5738
Segmentation fault (core dumped) mdrun -v -nt 12 -deffnm nvt-pr
I also get a bunch of .pdb files named accordingly to each step.
Could anyone explain to me what is going wrong? I can provide links to all
files if required.
Thanks again,
Nicholas
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