[gmx-users] How to combine Slipid FF with amber FF?

[Justin Lemkul]

On 8/31/14, 8:42 AM, Yorquant Wang wrote:
> Hi,
>     I have done that according to your advice and  when I do the command
> grompp, I get such a error:
> Fatal error:
> Atomtype NTL not found
> ---------------------
> this is my top file:
>
> #include "amber99sb-ildn.ff/forcefield.itp"
> #include "POPC.itp"
> #include "protein-amber.itp"
> #include "amber99sb-ildn.ff/ions.itp"
> #include "amber99sb-ildn.ff/tip3p.itp"
>

You get the error because none of these files knows anything about Slipids 
parameters except POPC.itp, which tries to use them.  So grompp fails.  See my 
previous reply; you need to modify the force field.

-Justin

> [ system ]
> ; Name
> membrane protein
> [ molecules ]
> ; Compound #mols
>
> protein          2
> POPC             72
> SOL               3337
> NA                  18
> CL                  22
>
>
>
>
> 2014-08-31 20:20 GMT+08:00 rajat desikan <rajatdesikan at gmail.com>:
>
>> Hi,
>>
>> Slipids are already compatible with Amber. Just download the proper
>> lipid.itp file (DPPC.itp, DMPC.itp, ...) from the Slipids website, and
>> include the below line in your .top after processing your protein with
>> pdb2gmx (and selecting some Amber FF).
>>
>> ; Include lipid topology
>> #include "./DMPC.itp"
>>
>> Of course, you can change the name of the lipid.itp according to the
>> lipids in your system.
>>
>> The order in which this appears in your .top matters. If you add the
>> lipids to your simulation box and then solvate it, the above line must
>> come prior to the water.itp
>>
>> Regards,
>>
>>
>> On 8/31/14, Yorquant Wang <wangykoo at gmail.com> wrote:
>>> Hi all,
>>>        I want to do a membrane protein simulation and I want to use amber
>> FF
>>> for protein (my target protein contains many beta sheet secondary
>>> structures). But forcefield.ff file in  the web:
>>> http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html, contains only
>>> lipids parameter. I don't know how to conbined those lipid parameter
>>> with amber99sb-ildn.ff.
>>>        Is there anybody who can help me? Thank you very much.
>>>
>>>
>>> --
>>> Yukun Wang
>>> PhD candidate
>>> Institute of Natural Sciences && College of Life Science, Shanghai Jiao
>>> Tong University
>>> Cell phone: 13621806236.
>>> China Shanghai
>>> --
>>> 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.
>>>
>>
>>
>> --
>> Rajat Desikan (Ph.D Scholar)
>> Prof. K. Ganapathy Ayappa's Lab (no 13),
>> Dept. of Chemical Engineering,
>> Indian Institute of Science, Bangalore
>> --
>> 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.
>>
>
>
>

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

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

==================================================