[gmx-users] grompp error

pandey at bioinfo.ernet.in pandey at bioinfo.ernet.in
Wed Aug 11 13:01:47 CEST 2004

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"
#include "spc.itp"
#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


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