[gmx-users] backmapping protein + dppc

[Tsjerk Wassenaar]

Hey :)

Right. The backmapping uses the atomistic topology, just like any MD based
protocol (well, and in another way too, but that's not relevant here). The
Tieleman lipids are not compatible with G53a6 just like that. You should be
able to find lipids for that FF from David Poger.

Justin, it's sure worth trying once ;)

Cheers,

Tsjerk
On Jan 27, 2015 6:20 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 1/27/15 8:55 AM, Adriana Garro wrote:
>
>> Hi Tsjerk,
>>
>> Yes, you are right,  it was :-)
>> But now a have a new error message
>>
>> Atomtype LC3 not found
>>
>> I have in the working directory:
>> dppc.itp (Dr. Tieleman website)
>> lipid.itp (Dr. Tieleman website)
>> gromos53a6_lipid.ff/ folder (with all the files modified according to
>> kalp-15 tutorial)
>>
>
> I don't know anything about these back-mapping protocols between CG and
> AA, but if you're getting an error related to an atom type not being found,
> that means you haven't fully constructed the force field correctly.  That
> error is usually triggered when the atom type in question is not present in
> ffnonbonded.itp.
>
> -Justin
>
>  topol-gromos53a6_lipid.ff.top
>> with
>> #include "gromos53a6_lipid.ff/forcefield.itp"
>> ; Include DPPC chain topology
>> #include "dppc.itp"
>> located in the correct place
>>
>> to prepare the atomistic topology I just used
>>
>> pdb2gmx -f protein-aa.pdb -ignh
>> then selected
>> gromos96-53A6
>>
>> Just the protein is in this file protein-aa.pdb (without lipids)
>> but then I edited the topology file adding the correct amount of DPPC in
>> agreement with the CG coordinates file, water and iones seem not be so
>> important here.
>>
>> Thanks for the help provided!
>> Cheers,
>>
>> Adriana
>>
>>
>>
>>
>>
>>
>>
>> ***********************************************************
>> Dra. Adriana D. Garro
>> Química Medicinal
>> Facultad de Química, Bioquímica y Farmacia
>> Universidad Nacional de San Luis
>> IMASL-CONICET
>> San Luis, Argentina
>>
>> Tel..............:+54 266 4424689 int 6153
>> e-mail...: adgarro at unsl.edu.ar
>> e-mail...:  adrianagarrosl at gmail.com
>>
>>
>> **********************************************************
>>
>> 2015-01-27 11:50 GMT+01:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:
>>
>>  Hi Adriana,
>>>
>>> The message says #include"gromos...
>>> I guess you meant to have a space between them.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Tue, Jan 27, 2015 at 11:31 AM, Adriana Garro <
>>> adrianagarrosl at gmail.com>
>>> wrote:
>>>
>>>  Dear gromacs users,
>>>>
>>>> I am trying to backmap my system which is protein + dppc lipids.
>>>> I built the atomistic topology file according to the KALP-15 tutorial
>>>> created by Justin Lemkul.
>>>> I have in my working directory a folder called gromos53a6_lipid.ff with
>>>>
>>> all
>>>
>>>> the files modified in line with the tutorial.
>>>> Then I used this command line
>>>>
>>>>   ./initram.sh -f reimaged_coord.gro -o aa_gromos96-53A6.gro -to
>>>>
>>> gromos53a6
>>>
>>>> -p topol-gromos53a6_lipid.ff.top
>>>>
>>>> and after several steps I have the following error message
>>>>
>>>> Program grompp, VERSION 4.6.3
>>>> Source code file: /usr/local/gromacs-4.6.3/src/kernel/topio.c, line:
>>>> 640
>>>>
>>>> Fatal error:
>>>> Syntax error - File backmapped.top, line 20
>>>> Last line read:
>>>> '#include"gromos53a6_lipid.ff/forcefield.itp"'
>>>>
>>>> I would really appreciate some advices in order to solve this.
>>>> Thanks in advance!
>>>>
>>>> Adriana
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>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
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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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