[gmx-users] converted topology from amber to gromacs

[Justin Lemkul]

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> 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> 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> 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.
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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

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