[gmx-users] Protein-Peptide Simulation help

Wed Dec 21 09:04:50 CET 2016

Thanks for your reply.

Azeem

On 12/21/16, gromacs.org_gmx-users-request at maillist.sys.kth.se
<gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
>    1. Re: Charge on drug (Justin Lemkul)
>    2. Re: Protein-Peptide Simulation help (Justin Lemkul)
>    3. Re: martini lipids self-assembly pressure coupling (Justin Lemkul)
>    4. Re: Should I restrain omega dihedrals or just phi/psi?
>       (Justin Lemkul)
>    5. Re: TIP3 water problem (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 20 Dec 2016 21:18:20 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Charge on drug
> Message-ID: <424fbea6-7255-9608-9e80-892995d8b801 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/19/16 1:23 PM, tasneem kausar wrote:
>> Thank you for reply
>> What type of refinements are needed in topolgy file.
>> I have created the topology file from pdb file. Mol2 was converted into
>> pdb
>> and sdf of pubchem was converted into mol2.
>> So sdf to mol2 to pdb.
>> And please suggest me the right choice of server for itp file generation.
>>
>
> Check the bond length parameters and make sure your coordinate file matches
> the
> order of the atoms in the topology.  Don't ignore warnings from grompp.
>
> -Justin
>
>> Thanks in advance
>>
>> On 19 Dec 2016 18:31, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>>
>>>
>>>
>>> On 12/19/16 5:31 AM, tasneem kausar wrote:
>>>>
>>>> Thanks for reply
>>>>
>>>> I have visualized solvate.gro and em.gro. Some bonds that are not
>>>> present
>>>> in box.gro is seen in em.gro.
>>>> I am giving you the link of the file to visualize.
>>>> https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE
>>>> https://drive.google.com/open?id=0B51QL37xf6MKMTByZmR1MURGTXM
>>>
>>>
>>> You have an amide group that distorts, bringing the carbonyl C closer to
>> the amide proton, which VMD then fictitiously assigns as a C-H bond.  The
>> C-N bond is much too short.  This suggests your topology is of
>> insufficient
>> quality for doing simulations and requires refinement.  There is, of
>> course, no actual bond there, as Mark has pointed out.  Visualization
>> software tries to guess where bonds should be based on interatomic
>> distances.  The topology is definitive. What you see on your screen is
>> not.
>>>
>>>
>>>> I addition to that I have done energy minimization multiple times with
>>>> steepest decent and conjugate gradient method. Potential energy value
>>>> is
>>>> negative in every minimization. When I am trying position restrain core
>>>> dump with multiple lincs warning occurs.
>>>
>>>
>>> Your topology needs work.  It will not be stable for any simulation.
>>>
>>> -Justin
>>>
>>>
>>>> Please tell me how this problem would be resolved
>>>>
>>>> On Mon, Dec 19, 2016 at 1:52 PM, Mark Abraham
>>>> <mark.j.abraham at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Your energy minimization literally cannot create bonds because those
>>>>> are
>>>>> already defined by your topology. See
>>>>>
>> http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#
>>>>> Topology_bonds_vs_Rendered_bonds
>>>>> for what's probably going on.
>>>>>
>>>>> Mark
>>>>>
>>>>> On Mon, 19 Dec 2016 19:05 tasneem kausar <tasneemkausar12 at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear All
>>>>>>
>>>>>>
>>>>>> I am using Acpype server to generate topology file of drug molecule
>>>>>> to
>>>>>> perform protein drug MD simulation. Acpype have generated the itp
>>>>>> file
>>>>>
>>>>> and
>>>>>>
>>>>>> other necessary for MD simulations. I am doing MD on gromacs 5.1.4
>>>>>
>>>>> software
>>>>>>
>>>>>> using amber99sb force field. When I have done energy minimization
>>>>>> some
>>>>>> unwanted bonds are formed in drug molecule. So the position restraint
>> is
>>>>>> not able to execute. The problem is due to the unusual bond in drug
>> atom.
>>>>>> When I used the itp file of PRODRG server position restraint goes
>>>>>> successfully. I have used the gromos54a7 ff. But there is problem
>>>>>> with
>>>>>
>>>>> the
>>>>>>
>>>>>> charge present on the atom that comes from PRODRG.
>>>>>>
>>>>>> Please tell me how charge on the atom can be corrected in itp file of
>>>>>> PRODRG.  How the problem in energy minimization with the Acpype itp
>> will
>>>>>
>>>>> be
>>>>>>
>>>>>> resolved.
>>>>>>
>>>>>> Thanks in Advance
>>>>>> With Regards
>>>>>> Tasneem
>>>>>> --
>>>>>> 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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>>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
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>>>>>
>>>
>>> --
>>> ==================================================
>>>
>>> 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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
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>> send a mail to gmx-users-request at gromacs.org.
>>
>
> --
> ==================================================
>
> 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: Tue, 20 Dec 2016 21:19:05 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Protein-Peptide Simulation help
> Message-ID: <b9a5f725-6094-d0ca-5689-f57fe54a7278 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/20/16 12:36 AM, Syed Azeem wrote:
>> Hello All,
>>
>> I'm trying to simulate a Protein-Peptide complex using GROMACS 5.1.4.
>> For reference, I referred Justin Lemkul's Tutorial for Protein Ligand
>> complexes. In which, the topology for ligand (small molecule) was
>> generated using PRODRG.
>>
>> In my case, do I need to treat my peptide (16-mer) in such a way? Or
>> just directly simulating the protein-peptide complex is good enough?
>>
>
> A peptide is a protein.  Do not use PRODRG or any other such tools; just
> build
> its topology with pdb2gmx using the normal force field.
>
> -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: Tue, 20 Dec 2016 21:19:31 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] martini lipids self-assembly pressure
> 	coupling
> Message-ID: <479e5fab-bed9-4345-5d17-1d7358634bf7 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/20/16 7:04 AM, Gmx QA wrote:
>> Hi all
>>
>> I am running a simulation with martini lipids with the lipids initially
>> placed randomly together with W solvent in a box. What pressure control
>> do
>> I apply?
>
> What do people do in published studies like this?  I would think it should
> be
> isotropic.
>
> -Justin
>
>>
>> I have tried isotropic, since the system indeed is isotropic initially,
>> but
>> I don't see formation of a bilayer, rather multiple layers of lipids
>> and/or
>> cylindrical weird structures. Going anisotropic always deforms the box,
>> it
>> becomes longer and longer in z until almost infinity. Semi-isotropic is
>> correct for bilayers obviously, but can I use that before the bilayer is
>> formed?
>>
>> Thanks
>> /PK
>>
>
> --
> ==================================================
>
> 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: Tue, 20 Dec 2016 21:20:56 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Should I restrain omega dihedrals or just
> 	phi/psi?
> Message-ID: <cc307876-17cc-d037-6c7b-3d9641573152 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/20/16 8:08 AM, Daniel Bauer wrote:
>> Hello,
>>
>> Im working on MD simulations of membrane proteins and want to restrain
>> the
>> backbone dihedrals of some amino acids. I now wonder if its sufficient to
>> restrain only phi/psi dihedrals as shown in the manual (
>> http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints), or if
>> I
>> should also set restrains on omega dihedrals?
>>
>
> Restraining omega will keep the peptide bonds from cis-trans isomerization,
>
> which is exceedingly rare under normal ambient conditions with most force
> fields; I don't see what restraining it would do.  If you want to preserve
> secondary structure elements, restrain phi and psi.
>
> -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: 5
> Date: Tue, 20 Dec 2016 21:24:24 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] TIP3 water problem
> Message-ID: <bf4cdf61-02be-1af9-b2ac-61951df5b745 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/20/16 2:41 PM, nikolaev at spbau.ru wrote:
>> Hi, all!
>>
>> I am working with the protein structure with internal waters of TIP3
>> type,
>> and running grompp ends with an error of "No default U-B types", as I
>> understand because of some internal inconsistency between atom types (H1,
>> H2 and OH2 in my tip3, HW1, HW2, OW in sol). I tried to rename atoms in
>> both topol.top and .gro files, add extra .itp file in charmm27.ff,
>> nothing
>> worked.
>>
>> However, this problem has already been mentioned here:
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/087725.html
>>
>> and the solution involved modifying top file (add waters information
>> manually). Is it really the only solution of this problem? Because as I
>> understand I need to insert manually all the charges, angles, bond lenths
>> for all the water molecules. And it seems quite a problem, if I want to
>> run more than 1 system.
>>
>
> Water molecules should not have [bonds] and [angles] directives because they
>
> should be treated as rigid via SETTLES.  If your topology has explicit bonds
> and
> angles, remove them and re-process the coordinates with pdb2gmx to prevent
> this
> spurious assignment.  Then just #include "tip3p.itp" and list the waters in
>
> [molecules].
>
> -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
>
> ==================================================
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
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