[gmx-users] backmapping protein + dppc

[Justin Lemkul]

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.
>> --
>> Gromacs Users mailing list
>>
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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

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