[gmx-users] Overriding atomtype O
Justin A. Lemkul
jalemkul at vt.edu
Sun Jun 20 13:24:05 CEST 2010
afsaneh maleki wrote:
> 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?
>
>
It looks like you've somehow duplicated your [atomtypes] directive or otherwise
mangled the topology. There is a tutorial on the Gromacs site that specifically
deals with membrane proteins and how to construct the topology. It may be
useful to you.
-Justin
>
> 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]:
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> Overriding atomtype O
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> WARNING 2 [file ffG53a6nb.itp, line 4]:
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> Overriding atomtype OM
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> WARNING 3 [file ffG53a6nb.itp, line 5]:
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> Overriding atomtype OA
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> WARNING 4 [file ffG53a6nb.itp, line 6]:
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> Overriding atomtype OE
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> WARNING 5 [file ffG53a6nb.itp, line 7]:
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> Overriding atomtype OW
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> WARNING 6 [file ffG53a6nb.itp, line 8]:
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> Overriding atomtype N
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> WARNING 7 [file ffG53a6nb.itp, line 9]:
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> Overriding atomtype NT
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> WARNING 8 [file ffG53a6nb.itp, line 10]:
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> Overriding atomtype NL
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> WARNING 9 [file ffG53a6nb.itp, line 11]:
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> Overriding atomtype NR
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> WARNING 10 [file ffG53a6nb.itp, line 12]:
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> Overriding atomtype NZ
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> WARNING 11 [file ffG53a6nb.itp, line 13]:
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> Overriding atomtype NE
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> WARNING 12 [file ffG53a6nb.itp, line 14]:
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> Overriding atomtype C
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> WARNING 13 [file ffG53a6nb.itp, line 15]:
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> Overriding atomtype CH0
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> WARNING 14 [file ffG53a6nb.itp, line 16]:
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> Overriding atomtype CH1
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> WARNING 15 [file ffG53a6nb.itp, line 17]:
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> Overriding atomtype CH2
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> WARNING 16 [file ffG53a6nb.itp, line 18]:
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> Overriding atomtype CH3
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> WARNING 17 [file ffG53a6nb.itp, line 19]:
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> Overriding atomtype CH4
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> WARNING 18 [file ffG53a6nb.itp, line 20]:
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> Overriding atomtype CH2r
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> WARNING 19 [file ffG53a6nb.itp, line 21]:
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> Overriding atomtype CR1
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> WARNING 20 [file ffG53a6nb.itp, line 22]:
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> Overriding atomtype HC
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> WARNING 21 [file ffG53a6nb.itp, line 23]:
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> Overriding atomtype H
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> WARNING 22 [file ffG53a6nb.itp, line 24]:
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> Overriding atomtype DUM
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> WARNING 23 [file ffG53a6nb.itp, line 25]:
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> Overriding atomtype S
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> WARNING 24 [file ffG53a6nb.itp, line 26]:
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> Overriding atomtype CU1+
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> WARNING 25 [file ffG53a6nb.itp, line 27]:
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> Overriding atomtype CU2+
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> WARNING 26 [file ffG53a6nb.itp, line 28]:
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> Overriding atomtype FE
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> WARNING 27 [file ffG53a6nb.itp, line 29]:
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> Overriding atomtype ZN2+
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> WARNING 28 [file ffG53a6nb.itp, line 30]:
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> Overriding atomtype MG2+
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> WARNING 29 [file ffG53a6nb.itp, line 31]:
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> Overriding atomtype CA2+
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> WARNING 30 [file ffG53a6nb.itp, line 32]:
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> Overriding atomtype P
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> WARNING 31 [file ffG53a6nb.itp, line 33]:
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> Overriding atomtype AR
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> WARNING 32 [file ffG53a6nb.itp, line 34]:
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> Overriding atomtype F
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> WARNING 33 [file ffG53a6nb.itp, line 35]:
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> Overriding atomtype CL
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> WARNING 34 [file ffG53a6nb.itp, line 36]:
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> Overriding atomtype BR
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> WARNING 35 [file ffG53a6nb.itp, line 37]:
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> Overriding atomtype CMet
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> WARNING 36 [file ffG53a6nb.itp, line 38]:
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> Overriding atomtype OMet
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> WARNING 37 [file ffG53a6nb.itp, line 39]:
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> Overriding atomtype NA+
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> WARNING 38 [file ffG53a6nb.itp, line 40]:
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> Overriding atomtype CL-
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> WARNING 39 [file ffG53a6nb.itp, line 41]:
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> Overriding atomtype CChl
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> WARNING 40 [file ffG53a6nb.itp, line 42]:
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> Overriding atomtype CLChl
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> WARNING 41 [file ffG53a6nb.itp, line 43]:
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> Overriding atomtype HChl
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> WARNING 42 [file ffG53a6nb.itp, line 44]:
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> Overriding atomtype SDmso
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> WARNING 43 [file ffG53a6nb.itp, line 45]:
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> Overriding atomtype CDmso
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> WARNING 44 [file ffG53a6nb.itp, line 46]:
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> Overriding atomtype ODmso
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> WARNING 45 [file ffG53a6nb.itp, line 47]:
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> Overriding atomtype CCl4
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> WARNING 46 [file ffG53a6nb.itp, line 48]:
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> Overriding atomtype CLCl4
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> WARNING 47 [file ffG53a6nb.itp, line 49]:
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> Overriding atomtype FTFE
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> WARNING 48 [file ffG53a6nb.itp, line 50]:
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> Overriding atomtype CTFE
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> WARNING 49 [file ffG53a6nb.itp, line 51]:
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> Overriding atomtype CHTFE
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> WARNING 50 [file ffG53a6nb.itp, line 52]:
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> Overriding atomtype OTFE
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> WARNING 51 [file ffG53a6nb.itp, line 53]:
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> Overriding atomtype CUrea
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> WARNING 52 [file ffG53a6nb.itp, line 54]:
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> Overriding atomtype OUrea
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> WARNING 53 [file ffG53a6nb.itp, line 55]:
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> Overriding atomtype NUrea
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> WARNING 54 [file ffG53a6nb.itp, line 56]:
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> Overriding atomtype SI
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> WARNING 55 [file ffG53a6nb.itp, line 57]:
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> Overriding atomtype MNH3
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> WARNING 56 [file ffG53a6nb.itp, line 58]:
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> Overriding atomtype MW
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>
> 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
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> Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
>
> Excluding 3 bonded neighbours molecule type 'protein'
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> turning all bonds into constraints...
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> Excluding 3 bonded neighbours molecule type 'DOPC'
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> turning all bonds into constraints...
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> Excluding 2 bonded neighbours molecule type 'SOL'
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> turning all bonds into constraints...
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> Excluding 1 bonded neighbours molecule type 'NA+'
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> turning all bonds into constraints...
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> Excluding 1 bonded neighbours molecule type 'CL-'
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> turning all bonds into constraints...
>
> processing coordinates...
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> double-checking input for internal consistency...
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> Reading position restraint coords from nvt-mutated_bi.gro
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> renumbering atomtypes...
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> converting bonded parameters...
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> initialising group options...
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> processing index file...
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> Making dummy/rest group for Acceleration containing 18916 elements
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> Making dummy/rest group for Freeze containing 18916 elements
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> 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
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> Making dummy/rest group for User2 containing 18916 elements
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> Making dummy/rest group for XTC containing 18916 elements
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> Making dummy/rest group for Or. Res. Fit containing 18916 elements
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> Making dummy/rest group for QMMM containing 18916 elements
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> T-Coupling has 3 element(s): Protein DOPC SOL_NA+_CL-
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> Energy Mon. has 1 element(s): rest
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> Acceleration has 1 element(s): rest
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> Freeze has 1 element(s): rest
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> User1 has 1 element(s): rest
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> User2 has 1 element(s): rest
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> VCM has 2 element(s): Protein_DOPC SOL_NA+_CL-
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> XTC has 1 element(s): rest
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> Or. Res. Fit has 1 element(s): rest
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> QMMM has 1 element(s): rest
>
> Checking consistency between energy and charge groups...
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> Calculating fourier grid dimensions for X Y Z
>
> Using a fourier grid of 48x45x48, spacing 0.152 0.160 0.154
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> Estimate for the relative computational load of the PME mesh part: 0.35
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> This run will generate roughly 3 Mb of data
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> writing run input file...
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>
>
> There were 56 warnings
>
>
>
> -------------------------------------------------------
>
> Program grompp, VERSION 4.0.5
>
> Source code file: gmx_fatal.c, line: 481
>
>
>
> Fatal error:
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> Too many warnings (56), grompp terminated.
>
> If you are sure all warnings are harmless, use the -maxwarn option.
>
>
>
>
>
> thanks in advance,
> Afsaneh
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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