[gmx-users] charmm36 lipid forcefield error

[Archana Sonawani-Jagtap]

Thanks for solving my error. But then do we need to remove the periodicity
of the bilayer obtained from charmm-gui?

Regards,

Archana

On Fri, Jun 2, 2017 at 2:24 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/1/17 4:43 PM, Archana Sonawani-Jagtap wrote:
>
>> Hi,
>>
>> I want to perform GPCR simulation in POPC bilayer using Charmm36
>> forcefield. I have generated the bilayer using CHARMM-GUI. I am following
>> GPCR tutorial by Justin (modified to GPCR by Anirban).
>>
>>
> CHARMM-GUI gives you the required force field files.  Use those and don't
> mess with them.
>
> I want to remove periodicity of the generated bilayer using following
>> command:
>>
>> grompp -f EM.mdp -c popc288.gro -p topol_popc.top -o EM.tpr
>> but I am getting below error:
>>
>> Program gmx grompp, VERSION 5.1
>>
>> Source code file:
>> /usr/local/gromacs-5.1/src/gromacs/gmxpreprocess/gmxcpp.c, line: 312
>>
>> Fatal error:
>>
>> Topology include file "charmm36_lipid.ff/forcefield.itp" not found
>>
>> I have downloaded Charmm36 FF from gromacs user's section and placed it in
>>
>>
> The force field files on gromacs.org are not authoritative CHARMM36 files
> and in fact contain a mixture of force field parameters (C36 for lipids,
> but C22+CMAP for protein, if I recall).  If you want correct C36
> parameters, get them from our website:
>
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>
> But again, CHARMM-GUI gave you everything you need, from the parent force
> field files all the way through the topology of the system, so you
> shouldn't have to touch any of this.
>
> -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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-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339