[gmx-users] converted topology from amber to gromacs

[mohammad r]

Thank you very much Justin 

    On Saturday, February 20, 2016 10:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 

 

On 2/20/16 8:49 AM, mohammad r wrote:
> Hi Justin,
>
> Thank you for your answer, I used grompp and it didn't give me error. I've
> attached a topology file of my systems. Can you please take a look at this and
> tell me your opinion? You mean that it doesn't make any problem when after
> conversion process the topology file doesn't refer to any force field?
>

The topology lists all needed parameters explicitly.  Note the header that says 
"This is a standalone topology."  "Standalone" means "I have everything you need 
right here."

The purpose of the #include function in GROMACS is to say "copy and paste the 
contents of the file here."  That is the same thing for grompp as listing all 
parameters explicitly.

There is no problem here with your topology.  It just looks a little different, 
but if you understand a little bit about how GROMACS assembles topologies, it 
becomes obvious that this is a slightly more verbose version of what you are 
used to seeing.

-Justin

> Thank you, Mohammad.
>
>
>
>
> On Friday, February 19, 2016 4:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 2/19/16 3:26 AM, mohammad r wrote:
>  >
>  > I don't know whether the problem is with the converting process (gromacs
> topology file doesn't refer to any force filed) or the the process of generating
> files in amber tools is wrong.
>  >
>
> Are you getting some specific problem in GROMACS?  ParmEd should give you a
> self-contained topology file that explicitly lists the parameters it uses.  It
> may not fit the convention of the normal sequence of #include statements because
> it's using a slightly different, but equally valid, approach.
>
> Without seeing your topology, it's impossible to figure out if there is any
> problem.  grompp is the quickest test here.  If it doesn't complain, you're fine.
>
> -Justin
>
>  >      On Friday, February 19, 2016 11:04 AM, mohammad r
> <mohammad.r0325 at yahoo.com <mailto:mohammad.r0325 at yahoo.com>> wrote:
>  >
>  >
>  >  #yiv7024757511 p
> {margin-bottom:0.1in;direction:ltr;line-height:120%;text-align:justify;}#yiv7024757511
> p.yiv7024757511western {font-size:12pt;}#yiv7024757511 p.yiv7024757511cjk
> {font-size:12pt;}#yiv7024757511 p.yiv7024757511ctl {font-size:12pt;}I used
> ff14SBAmber protein force field, #yiv7024757511 p
> {margin-bottom:0.1in;direction:ltr;line-height:120%;text-align:justify;}#yiv7024757511
> p.yiv7024757511western {font-size:12pt;}#yiv7024757511 p.yiv7024757511cjk
> {font-size:12pt;}#yiv7024757511 p.yiv7024757511ctl {font-size:12pt;}
> LIPID11force field and TIP3P water model. First I  loaded the force fields and
> water model then loaded the pdb file and finally I saved the topology and
> coordinate files.
>
>  >
>  >
>  >      On Friday, February 19, 2016 10:40 AM, Hai Nguyen <nhai.qn at gmail.com
> <mailto:nhai.qn at gmail.com>> wrote:
>  >
>  >
>  >  Hi
>  > You should know which AMBER force field when you made the topology file. (How
> did you make it?)
>  > Hai
>  > On Fri, Feb 19, 2016 at 12:56 AM, mohammad r <mohammad.r0325 at yahoo.com
> <mailto:mohammad.r0325 at yahoo.com>> wrote:
>  >
>  > Hi gromacs users,
>  > I've generatedinitial structure of my system by using ambertools (topology
> andcoordinate files) and converted it to gromacs format (.gro and .top)by
> parmed, but in topology file it doesn't refer to any forcefield.Does it make any
> problem in the results or it is ok? Because when Icompare the simulation result
> with experiment it is incorrect.
>  > Thank you, Mohammad.
>  > --
>  > Gromacs Users mailing list
>  >
>  > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>before posting!
>  >
>  > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  >
>  > * For (un)subscribe requests visit
>  > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>or send a
> mail to gmx-users-request at gromacs.org. <mailto: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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

-- 
==================================================

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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.