[gmx-users] grompp error

[pandey at bioinfo.ernet.in]

Hi All and Itamar Kass,

Thanks for reply.
I am using the ffgmx_lipids.tar.gz from the Gromacs site.
My main problem pertains to grompp run.


Error:
-----------------------------------------
Cleaning up temporary file gromppd7plu8
>> Fatal error: [ file "/home/pandey/tarfiles/lipid_gro/posre.itp", line
>> 42 ]:
>>              Atom index (51) in position_restraints out of bounds
>> (1-50)

-------------------------------------------
cheers

Pandey
Research Associate
Bioinforamtics Center
Univeristy of Pune
India
>     Look at the gromacs site (at
> http://www.gromacs.org/topologies/force_fields.php), Bert de Groot put
> a file named 'ffgmx_lipids.tar.gz' which hold the lipid param, use it.
> On Aug 11, 2004, at 2:01 PM, pandey at bioinfo.ernet.in wrote:
>
>>
>> Hi All,
>>
>> I am working on membrane peptides simulation under lipid (DPPC, from
>> Peter
>> Tieleman group site). I have downloaded the lipid and dppc .itp from
>> the
>> same site.
>>
>> 1) I am using the ffgmx.itp as suggested in mailing list in. My
>> topology
>> file look like:
>> -----------------
>> #include "/home/pandey/tarfiles/lipid_gro/ffgmx.itp"
>> #include "/home/pandey/tarfiles/lipid_gro/dppc.itp"
>> #include "/home/pandey/tarfiles/lipid_gro/posre.itp"
>>
>> #ifdef FLEX_SPC
>> #include "flexspc.itp"
>> #else
>> #include "spc.itp"
>> #endif
>> #include "/home/pandey/tarfiles/lipid_gro/dppc.itp"
>> [ system ]
>> ; name
>> [ molecules ]
>> ; name  number
>> DPPC    128
>> SOL    3655
>> Protein 1
>>
>>
>> --------------------------------------------------------
>>
>>
>> 2) If i include lipid.itp, it gives error of second dirrective. I tried
>> permutation of #include lipid.itp, #include dppc.itp, #include
>> posre.itp
>> (in same order), then error of LC3 or C not found comes. Then, I have
>> used
>> the order of includes in above mentioned *.top file.
>> But, when i run grompp with appropriate parameter, i get following
>> error:
>>
>> ----------------------
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
>> checking input for internal consistency...
>> calling /lib/cpp...
>> processing topology...
>> Generated 1174 of the 2016 non-bonded parameter combinations
>> Cleaning up temporary file gromppd7plu8
>> Fatal error: [ file "/home/pandey/tarfiles/lipid_gro/posre.itp", line
>> 42 ]:
>>              Atom index (51) in position_restraints out of bounds
>> (1-50)
>>
>> --------------------------------------------------------
>>
>> 3) One of solution mentioned in mailing list was include posre_lipid.
>> Then, I tried generate posre_lipid from pdb2gmx using G43a2x force
>> field.
>> But, there also it gives error like:
>>
>> DPP residue not found in *.rtp file.
>>
>> Then, I edited the *.rtp file by simply copying the content of dppc.itp
>> file in *.rtp file with some edition. But, again some error like:
>> ------------------------
>> All occupancies are one
>> Opening library file /usr/local/share/gromacs/top/ffG43a2x.atp
>> Atomtype 49
>> Reading residue database... (ffG43a2x)
>> Opening library file /usr/local/share/gromacs/top/ffG43a2x.rtp
>> Using default: not generating all possible dihedrals
>> Using default: excluding 3 bonded neighbors
>> Using default: generating 1,4 H--H interactions
>> Using default: removing impropers on same bond as a proper
>> Residue 13Fatal error: in .rtp file in residue DPPC at line:
>>      1     LC3       1    DPPC      C1       0         0.4000   15.0350
>>
>> ------------------------
>>
>> Any help will be highly appreceiated
>>
>> Cheers
>> pandey
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>
>
>
> ********************************************
> Computers are like airconditioners... They don't work well with Windows
> open.
> ********************************************
>
> ===========================================
> | Itamar Kass
> | The Alexander Silberman
> | Institute of Life Sciences
> | Department of Biological Chemistry
> | The Hebrew University, Givat-Ram
> | Jerusalem, 91904, Israel
> | Tel: +972-(0)2-6585146
> | Fax: +972-(0)2-6584329
> | Email: ikass at cc.huji.ac.il
> | Homepage:
> http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
> ============================================
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