[gmx-users] grompp error

[Itamar Kass]

    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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********************************************
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********************************************

===========================================
| 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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