Hi,
I have a problem with grompp. I want to simulate membrane protein. I adjust the [ molecules ] section to list the number and type of my components I run grompp and it shows 56 warning about all of atom types in ffG53a6nb.itp (56 atom types are in ffG53a6). I run pdb2gmx for protein only. Why does it give me these warning? I paste warning here: Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp WARNING 1 [file ffG53a6nb.itp, line 3]: Overriding atomtype O WARNING 2 [file ffG53a6nb.itp, line 4]: Overriding atomtype OM WARNING 3 [file ffG53a6nb.itp, line 5]: Overriding atomtype OA WARNING 4 [file ffG53a6nb.itp, line 6]: Overriding atomtype OE WARNING 5 [file ffG53a6nb.itp, line 7]: Overriding atomtype OW WARNING 6 [file ffG53a6nb.itp, line 8]: Overriding atomtype N WARNING 7 [file ffG53a6nb.itp, line 9]: Overriding atomtype NT WARNING 8 [file ffG53a6nb.itp, line 10]: Overriding atomtype NL WARNING 9 [file ffG53a6nb.itp, line 11]: Overriding atomtype NR WARNING 10 [file ffG53a6nb.itp, line 12]: Overriding atomtype NZ WARNING 11 [file ffG53a6nb.itp, line 13]: Overriding atomtype NE WARNING 12 [file ffG53a6nb.itp, line 14]: Overriding atomtype C WARNING 13 [file ffG53a6nb.itp, line 15]: Overriding atomtype CH0 WARNING 14 [file ffG53a6nb.itp, line 16]: Overriding atomtype CH1 WARNING 15 [file ffG53a6nb.itp, line 17]: Overriding atomtype CH2 WARNING 16 [file ffG53a6nb.itp, line 18]: Overriding atomtype CH3 WARNING 17 [file ffG53a6nb.itp, line 19]: Overriding atomtype CH4 WARNING 18 [file ffG53a6nb.itp, line 20]: Overriding atomtype CH2r WARNING 19 [file ffG53a6nb.itp, line 21]: Overriding atomtype CR1 WARNING 20 [file ffG53a6nb.itp, line 22]: Overriding atomtype HC WARNING 21 [file ffG53a6nb.itp, line 23]: Overriding atomtype H WARNING 22 [file ffG53a6nb.itp, line 24]: Overriding atomtype DUM WARNING 23 [file ffG53a6nb.itp, line 25]: Overriding atomtype S WARNING 24 [file ffG53a6nb.itp, line 26]: Overriding atomtype CU1+ WARNING 25 [file ffG53a6nb.itp, line 27]: Overriding atomtype CU2+ WARNING 26 [file ffG53a6nb.itp, line 28]: Overriding atomtype FE WARNING 27 [file ffG53a6nb.itp, line 29]: Overriding atomtype ZN2+ WARNING 28 [file ffG53a6nb.itp, line 30]: Overriding atomtype MG2+ WARNING 29 [file ffG53a6nb.itp, line 31]: Overriding atomtype CA2+ WARNING 30 [file ffG53a6nb.itp, line 32]: Overriding atomtype P WARNING 31 [file ffG53a6nb.itp, line 33]: Overriding atomtype AR WARNING 32 [file ffG53a6nb.itp, line 34]: Overriding atomtype F WARNING 33 [file ffG53a6nb.itp, line 35]: Overriding atomtype CL WARNING 34 [file ffG53a6nb.itp, line 36]: Overriding atomtype BR WARNING 35 [file ffG53a6nb.itp, line 37]: Overriding atomtype CMet WARNING 36 [file ffG53a6nb.itp, line 38]: Overriding atomtype OMet WARNING 37 [file ffG53a6nb.itp, line 39]: Overriding atomtype NA+ WARNING 38 [file ffG53a6nb.itp, line 40]: Overriding atomtype CL- WARNING 39 [file ffG53a6nb.itp, line 41]: Overriding atomtype CChl WARNING 40 [file ffG53a6nb.itp, line 42]: Overriding atomtype CLChl WARNING 41 [file ffG53a6nb.itp, line 43]: Overriding atomtype HChl WARNING 42 [file ffG53a6nb.itp, line 44]: Overriding atomtype SDmso WARNING 43 [file ffG53a6nb.itp, line 45]: Overriding atomtype CDmso WARNING 44 [file ffG53a6nb.itp, line 46]: Overriding atomtype ODmso WARNING 45 [file ffG53a6nb.itp, line 47]: Overriding atomtype CCl4 WARNING 46 [file ffG53a6nb.itp, line 48]: Overriding atomtype CLCl4 WARNING 47 [file ffG53a6nb.itp, line 49]: Overriding atomtype FTFE WARNING 48 [file ffG53a6nb.itp, line 50]: Overriding atomtype CTFE WARNING 49 [file ffG53a6nb.itp, line 51]: Overriding atomtype CHTFE WARNING 50 [file ffG53a6nb.itp, line 52]: Overriding atomtype OTFE WARNING 51 [file ffG53a6nb.itp, line 53]: Overriding atomtype CUrea WARNING 52 [file ffG53a6nb.itp, line 54]: Overriding atomtype OUrea WARNING 53 [file ffG53a6nb.itp, line 55]: Overriding atomtype NUrea WARNING 54 [file ffG53a6nb.itp, line 56]: Overriding atomtype SI WARNING 55 [file ffG53a6nb.itp, line 57]: Overriding atomtype MNH3 WARNING 56 [file ffG53a6nb.itp, line 58]: Overriding atomtype MW Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 825 of the 2346 non-bonded parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Excluding 3 bonded neighbours molecule type 'protein' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'DOPC' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA+' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL-' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... Reading position restraint coords from nvt-mutated_bi.gro renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Making dummy/rest group for Acceleration containing 18916 elements Making dummy/rest group for Freeze containing 18916 elements Making dummy/rest group for Energy Mon. containing 18916 elements Number of degrees of freedom in T-Coupling group Protein is 724.85 Number of degrees of freedom in T-Coupling group DOPC is 13622.15 Number of degrees of freedom in T-Coupling group SOL_NA+_CL- is 23613.00 Making dummy/rest group for User1 containing 18916 elements Making dummy/rest group for User2 containing 18916 elements Making dummy/rest group for XTC containing 18916 elements Making dummy/rest group for Or. Res. Fit containing 18916 elements Making dummy/rest group for QMMM containing 18916 elements T-Coupling has 3 element(s): Protein DOPC SOL_NA+_CL- 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 2 element(s): Protein_DOPC SOL_NA+_CL- 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... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 48x45x48, spacing 0.152 0.160 0.154 Estimate for the relative computational load of the PME mesh part: 0.35 This run will generate roughly 3 Mb of data writing run input file... There were 56 warnings ------------------------------------------------------- Program grompp, VERSION 4.0.5 Source code file: gmx_fatal.c, line: 481 Fatal error: Too many warnings (56), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. thanks in advance, Afsaneh
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