[gmx-users] Overriding atomtype O

afsaneh maleki maleki.afsaneh at gmail.com
Sun Jun 20 12:21:52 CEST 2010 

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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