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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