[gmx-users] grompp error in running simulation of lipid bilayer

[nitu sharma]

Hi pawan ,

          Thanks for your right suggestion bu t after editing lipid.itp the
another error comes like this-

processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 1369 of the 2211 non-bonded parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/flexspc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Excluding 3 bonded neighbours molecule type 'DMPC'
Excluding 2 bonded neighbours molecule type 'SOL'
processing coordinates...
Warning: atom name 1 in dmpc.top and dmpc-box.pdb does not match (CN1 - C1)
Warning: atom name 2 in dmpc.top and dmpc-box.pdb does not match (CN2 - C2)
Warning: atom name 3 in dmpc.top and dmpc-box.pdb does not match (CN3 - C3)
Warning: atom name 4 in dmpc.top and dmpc-box.pdb does not match (NTM - N4)
Warning: atom name 5 in dmpc.top and dmpc-box.pdb does not match (CA - C5)
Warning: atom name 6 in dmpc.top and dmpc-box.pdb does not match (CB - C6)
Warning: atom name 7 in dmpc.top and dmpc-box.pdb does not match (OA - O7)
Warning: atom name 8 in dmpc.top and dmpc-box.pdb does not match (P - P8)
Warning: atom name 9 in dmpc.top and dmpc-box.pdb does not match (OB - O9)
Warning: atom name 10 in dmpc.top and dmpc-box.pdb does not match (OC - O10)
Warning: atom name 11 in dmpc.top and dmpc-box.pdb does not match (OD - O11)
Warning: atom name 12 in dmpc.top and dmpc-box.pdb does not match (CC - C12)
Warning: atom name 13 in dmpc.top and dmpc-box.pdb does not match (CD - C13)
Warning: atom name 14 in dmpc.top and dmpc-box.pdb does not match (OE - O14)
Warning: atom name 15 in dmpc.top and dmpc-box.pdb does not match (C2A -
C15)
Warning: atom name 16 in dmpc.top and dmpc-box.pdb does not match (OF - O16)
Warning: atom name 17 in dmpc.top and dmpc-box.pdb does not match (C2B -
C17)
Warning: atom name 18 in dmpc.top and dmpc-box.pdb does not match (C2C -
C18)
Warning: atom name 19 in dmpc.top and dmpc-box.pdb does not match (C2D -
C19)
Warning: atom name 20 in dmpc.top and dmpc-box.pdb does not match (C2E -
C20)
(more than 20 non-matching atom names)

WARNING 1 [file dmpc.top, line 20]:
  5888 non-matching atom names
  atom names from dmpc.top will be used
  atom names from dmpc-box.pdb will be ignored
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are:  3783      OTHER residues
There are:     0    PROTEIN residues
There are:     0        DNA residues
Analysing Other...
Making dummy/rest group for T-Coupling containing 16853 elements
Making dummy/rest group for Acceleration containing 16853 elements
Making dummy/rest group for Freeze containing 16853 elements
Making dummy/rest group for Energy Mon. containing 16853 elements
Making dummy/rest group for VCM containing 16853 elements
Number of degrees of freedom in T-Coupling group rest is 50556.00
Making dummy/rest group for User1 containing 16853 elements
Making dummy/rest group for User2 containing 16853 elements
Making dummy/rest group for XTC containing 16853 elements
Making dummy/rest group for Or. Res. Fit containing 16853 elements
Making dummy/rest group for QMMM containing 16853 elements
T-Coupling       has 1 element(s): rest
Energy Mon.      has 1 element(s): rest
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
QMMM             has 1 element(s): rest
Checking consistency between energy and charge groups...

NOTE 1 [file em.mdp, line unknown]:
  You are using a plain Coulomb cut-off, this will often produce artifacts.
  You might want to consider using PME electrostatics.


This run will generate roughly 2 Mb of data
writing run input file...

There was 1 note

There was 1 warning

-------------------------------------------------------
Program grompp, VERSION 4.0.3
Source code file: gmx_fatal.c, line: 481

Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
-----------------------------------------------------
If u know the solution of this problem please let me know.


Thanks in advance.

Nitu Sharma
School of life sciences
Jawaherlal Nehru University
New Delhi India
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