[gmx-users] Re: Preparation of the pure lipid system with charmm force field

[James Starlight]

Justin,

In that way there was only one point wich was not understood for me


In charmm I already have lipids.rtp with the parametries for my lipids. Also
I have a single molecule of my lipid.
How via pdb2gmx I could create parametrised itp file except of posre.itp ?

James

2011/10/21 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> James Starlight wrote:
>
>> I've excluded   "charmm36.ff/lipids.rtp" from my topology and obtain new
>> error
>> Fatal error:
>> No such moleculetype POPC
>>
>> How I could include topology on this lipids ( all of them are present in
>> the lipids.rtp. ) ?
>> I have itp for the lipids only for the GROMOS ff so it should not be used
>> here
>>
>>
> I presented the details of this procedure to you already:
>
> http://lists.gromacs.org/**pipermail/gmx-users/2011-**October/065311.html<http://lists.gromacs.org/pipermail/gmx-users/2011-October/065311.html>
>
> -Justin
>
>
>> James
>>
>>
>> 2011/10/21 Mark Abraham <Mark.Abraham at anu.edu.au <mailto:
>> Mark.Abraham at anu.edu.**au <Mark.Abraham at anu.edu.au>>>
>>
>>
>>    On 21/10/2011 5:41 PM, James Starlight wrote:
>>
>>        I've also tried to make topology for my system parametriesed for
>>        charmm36 ff by hands but failed too :(
>>
>>        This is my topology for the POPC bilayer wich I've made in VMD
>>        membrane builder as well as downloaded a pre built membrane
>>        system ( I've tested for both cases)
>>
>>        ; Include chain topologies
>>        #include "charmm36.ff/forcefield.itp"
>>
>>        ; Include lipids
>>        #include "charmm36.ff/lipids.rtp"
>>
>>
>>    .rtp files may not be #included
>>
>>
>>
>>
>>        ; Include water topology
>>        #include "/charmm36.ff/tip3p.itp"
>>
>>
>>    Initial backslash refers to the root of your file system, so is
>>    likely wrong.
>>
>>
>>
>>        ; Include ion topologies
>>        #include "charmm36.ff/ions.itp"
>>
>>        ; System specifications
>>        [ system ]
>>        128-Lipid POPC Bilayer in water
>>
>>        [ molecules ]
>>        POPC 72
>>
>>        When I've loaded my molecule to grompp I've obtained error
>>
>>        Program grompp, VERSION 4.5.4
>>        Source code file: /tmp/gromacs-4.5.4/src/kernel/**__toppush.c,
>>
>>        line: 770
>>
>>        Fatal error:
>>        Unknown bond_atomtype 1
>>
>>        What does it means? Is here anybody who also tried to
>>        parametriesed theis lipids by charmm ff ?
>>
>>
>>    Don't blame the ff yet :-)
>>
>>    Mark
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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