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

Mon Mar 30 12:02:17 CEST 2009

Hello Madam,

Greetings from Pawan.
The solution for this is to edit the atom names as required such as replace
NTM  with N4 in all the places wherever NTM occurs.
Similarly do this for all the atoms of the dppc lipid.
I think this is a probable solution.
I dont know how far I am right.

Regards,
Pawan

2009/3/30 nitu sharma <sharmanitu35 at gmail.com>

> 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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