[gmx-users] Diagnosing + system blowing up

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Jul 31 23:21:36 CEST 2012


Thanks for dear Mark's suggestions.

What's the typical solution to fix such errors of grompp?
I don't have any idea to do what, so erased the lines defined in output of grompp, then I went through the NVT equilibrium, it didn't stop by multiple interaction errors. I don't know what will happen for the rest of the investigation, put the protein in bilayer and then Umbrella Sampling and .............  .
If anybody has suggestion, it would be appreciated.


Sincerely,
Shima


________________________________
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, July 31, 2012 4:49 AM
Subject: Re: [gmx-users] Diagnosing + system blowing up

I edited the grompp output and sent it to you. Bring that again here:
  Generated 21528 of the 21528 non-bonded parameter combinations
 Generating 1-4 interactions: fudge = 1
 Generated 18355 of the 21528 1-4 parameter combinations

 ERROR 1 [file topol.top, line 414]:
      No default Bond types


 ERROR 2 [file topol.top, line 1698]:
      No default U-B types


 ERROR 3 [file topol.top, line 1699]:
      No default U-B types


 ERROR 4 [file topol.top, line 2345]:
      No default Proper Dih. types


 ERROR 5 [file topol.top, line 2346]:
      No default Proper Dih. types

 ERROR 6 [file topol.top, line 3278]:
      No default Improper Dih. types

And wrote line 414 is :
line 414 of topol.tp:
   [bonds]
         1     2     1



Sincerely,
Shima


________________________________
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, July 31, 2012 4:40 AM
Subject: Re: [gmx-users] Diagnosing + system blowing up

On 31/07/2012 7:16 AM, Shima Arasteh wrote:
> Wow!  That was a fabulous explanation given to me. Thanks dear Mark! :-)
>
> I regenerated the topol.top to check the correctness of input and FF files. Some output has been changed however a little bit. Now, I bring you all was needed again:
>
>> 1. rtp entry
>>
>> [ FVAL ]
>   [ atoms ]
>      CN    C     0.357    0
>      ON    O    -0.51    1
>      H1    HA    0.100    2
>      N    NH1    -0.423    3
>      HN    H    0.333    4
>      CA    CT1    0.034    5
>      HA    HB    0.09    6
>      CB    CT1    -0.093    7
>      HB    HA    0.09    8
>      CG1    CT3    -0.268    9
>      HG11    HA    0.09    10
>      HG12    HA    0.09    11
>      HG13    HA    0.09    12
>      CG2    CT3    -0.268    13
>      HG21    HA    0.09    14
>      HG22    HA    0.09    15
>      HG23    HA    0.09    16
>      C    C    0.528    17
>      O    O    -0.510    18
>   [ bonds ]
>      CN    H1
>      CN    ON
>      CN    N
>      N    HN
>      CA    N
>      CA    HA
>      CA    C
>      C    O
>      CA    CB
>      CB    HB
>      CB    CG1
>      CB    CG2
>      CG2    HG21
>      CG2    HG22
>      CG2    HG23
>      CG1    HG11
>      CG1    HG12
>      CG1    HG13
>      
>   [ impropers ]
>      CN     N    ON    H1
>
>> 2. hdb entry
> In which file?
> *aminoacids.hdb
>
>
>> FVAL    6
>> 1    1    H1    CN    N    ON
> This should be generating H1 bonded to CN...
>
>> 1    1    HN    N    C    CA
>> 1    5    HA    CA    N    C    CB
>> 1    5    HB    CB    CA    CG1    CG2
>> 3    4    HG1    CG1    CB    CA
>> 3    4    HG2    CG2    CB    CA
>>
>> 3. N-terminal fragment
>> HETATM    1  CN  FVAL    1      -0.721   1.600   1.249
>> HETATM    2  ON  FVAL    1      -0.839   2.806   1.453
>> ATOM      3  N   FVAL    1      -1.227   0.728   2.125
>> ATOM      4  CA  FVAL    1      -1.918   1.159   3.323
>> ATOM      5  C   FVAL    1      -1.969   2.678   3.410
>> ATOM      6  O   FVAL    1      -0.931   3.335   3.447
>> ATOM      7  CB  FVAL    1      -1.219   0.644   4.576
>> ATOM      8  CG1 FVAL    1       0.208   1.178   4.618
>> ATOM      9  CG2 FVAL    1      -1.976   1.118   5.812
>>
>> 4. pdb2gmx command
>> #pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter
>>
>> 5. pdb2gmx output
> Using the Charmm36-modified force field in directory ./charmm36-modified.ff
>
> Opening force field file ./charmm36-modified.ff/aminoacids.r2b
> Opening force field file ./charmm36-modified.ff/rna.r2b
> Reading monomer.pdb...
> Read 177 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 24 residues with 177 atoms
>
>    chain  #res #atoms
>    1 ' '    24    177
>
> All occupancy fields zero. This is probably not an X-Ray structure
> Opening force field file ./charmm36-modified.ff/atomtypes.atp
> Atomtype 1
> Reading residue database... (charmm36-modified)
> Opening force field file ./charmm36-modified.ff/aminoacids.rtp
> Residue 42
> Sorting it all out...
> Opening force field file ./charmm36-modified.ff/dna.rtp
> Residue 46
> Sorting it all out...
> Opening force field file ./charmm36-modified.ff/lipids.rtp
> Residue 82
> Sorting it all out...
> Opening force field file ./charmm36-modified.ff/rna.rtp
> Residue 86
> Sorting it all out...
> Opening force field file ./charmm36-modified.ff/aminoacids.hdb
> Opening force field file ./charmm36-modified.ff/dna.hdb
> Opening force field file ./charmm36-modified.ff/lipids.hdb
> Opening force field file ./charmm36-modified.ff/rna.hdb
> Opening force field file ./charmm36-modified.ff/aminoacids.n.tdb
> Opening force field file ./charmm36-modified.ff/dna.n.tdb
> Opening force field file ./charmm36-modified.ff/rna.n.tdb
> Opening force field file ./charmm36-modified.ff/aminoacids.c.tdb
> Opening force field file ./charmm36-modified.ff/dna.c.tdb
> Opening force field file ./charmm36-modified.ff/rna.c.tdb
>
> Back Off! I just backed up topol.top to ./#topol.top.2#
> Processing chain 1 (177 atoms, 24 residues)
> Identified residue FVAL1 as a starting terminus.
> Identified residue GLY24 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Select start terminus type for FVAL-1
>   0: NH3+
>   1: NH2
>   2: None
> 2
> Start terminus FVAL-1: None
> Select end terminus type for GLY-24
>   0: COO-
>   1: COOH
>   2: CT2
>   3: CT3
>   4: None
> 0
> End terminus GLY-24: COO-
> Opening force field file ./charmm36-modified.ff/aminoacids.arn
> Opening force field file ./charmm36-modified.ff/dna.arn
> Opening force field file ./charmm36-modified.ff/rna.arn
> Checking for duplicate atoms....
> Now there are 24 residues with 360 atoms
> Making bonds...
> Number of bonds was 362, now 362
> Generating angles, dihedrals and pairs...
> Before cleaning: 925 pairs
> Before cleaning: 930 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...There are   22 cmap torsion pairs
> There are  930 dihedrals,   49 impropers,  644 angles
>             916 pairs,      362 bonds and     0 virtual sites
> Total mass 2510.906 a.m.u.
> Total charge 1.000 e
> Writing topology
>
> Back Off! I just backed up posre.itp to ./#posre.itp.1#
>
> Writing coordinate file...
>
> Back Off! I just backed up monomer.gro to ./#monomer.gro.1#
>                  --------- PLEASE NOTE ------------
> You have successfully generated a topology from: monomer.pdb.
> The Charmm36-modified force field and the tip3p water model are used.
>                  --------- ETON ESAELP ------------
>
>
>> 6. N-terminal fragment of the grompp -c input
>      1FVAL    CN    1   3.039   1.904   2.416
>      1FVAL    H1    2   3.086   1.871   2.334

This H1 atom is now in the right position for generation from the 
correct .hdb, and pdb2gmx is not complaining of the long bond to H1, 
which I think means you are using the correct .hdb now, and were not 
doing so earlier. So my suggestion of a bug was unfounded.

>      1FVAL    ON    3   3.027   2.025   2.436
>      1FVAL     N    4   2.988   1.817   2.504
>      1FVAL    HN    5   3.029   1.759   2.433
>      1FVAL    CA    6   2.919   1.860   2.623
>      1FVAL    HA    7   2.828   1.821   2.614
>      1FVAL    CB    8   2.989   1.808   2.749
>      1FVAL    HB    9   2.991   1.708   2.747
>      1FVAL   CG1   10   3.132   1.862   2.753
>      1FVAL  HG11   11   3.178   1.828   2.835
>      1FVAL  HG12   12   3.181   1.831   2.672
>      1FVAL  HG13   13   3.130   1.962   2.754
>      1FVAL   CG2   14   2.913   1.856   2.872
>      1FVAL  HG21   15   2.959   1.822   2.954
>      1FVAL  HG22   16   2.911   1.956   2.874
>      1FVAL  HG23   17   2.820   1.821   2.869
>      1FVAL     C   18   2.914   2.012   2.632
>      1FVAL     O   19   3.018   2.077   2.636
>
> ... and this shows atom H1 around 0.1nm from atom C. I can think of no
> legitimate reason how this could occur, given your stated .hdb, but I
> seem to recall an old .hdb version you showed had a line
>
> 1    1    H1    C    N    ON
>
> rather than the correct
>
> 1    1    H1    CN    N    ON
>
> ********* I checked it, there was the correct one.
>
> and this would explain the weird H1 position perfectly (but not how it still gets bonded to atom 1). I'd like you to double check that ./charmm36-modified.ff/aminoacids.hdb has (only) the correct FVAL entry. Also, I'd like to see the first 30 or so lines of the [bonds] section of this [moleculetype] in topol.top, so we can really see what bonds are generated.
>
> * First 50 lines of the [bonds] section:

These are now normal. I suspect they were not earlier.

>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>      1     2     1
>      1     3     1
>      1     4     1
>      4     5     1
>      4     6     1
>      6     7     1
>      6     8     1
>      6    18     1
>      8     9     1
>      8    10     1
>      8    14     1
>     10    11     1
>     10    12     1
>     10    13     1
>     14    15     1
>     14    16     1
>     14    17     1
>     18    19     1
>     20    21     1
>     20    22     1
>     22    23     1
>     22    24     1
>     22    29     1
>     24    25     1
>     24    26     1
>     24    27     1
>     27    28     1
>     29    30     1
>     29    31     1
>     31    32     1
>     31    33     1
>     33    34     1
>     33    35     1
>     33    48     1
>     35    36     1
>     35    37     1
>     35    38     1
>     38    39     1
>     38    40     1
>     38    44     1
>     40    41     1
>     40    42     1
>     40    43     1
>     44    45     1
>     44    46     1
>     44    47     1
>     48    49     1
>     48    50     1
>     50    51     1
>     50    52     1
>
>
> I think you may have encountered a new bug in pdb2gmx.
>
>>        1FVAL     O   19   3.019   2.076   2.635
>>
>> 7.grompp command line
>> # grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr
>>
>>
>> 8. grompp output
>> Generated 21528 of the 21528 non-bonded parameter combinations
>> Generating 1-4 interactions: fudge = 1
>> Generated 18355 of the 21528 1-4 parameter combinations
>>
>> ERROR 1 [file topol.top, line 414]:
>>      No default Bond types
>>
>>
>> ERROR 2 [file topol.top, line 1698]:
>>      No default U-B types
>>
>>
>> ERROR 3 [file topol.top, line 1699]:
>>      No default U-B types
>>
>>
>> ERROR 4 [file topol.top, line 2345]:
>>      No default Proper Dih. types
>>
>>
>> ERROR 5 [file topol.top, line 2346]:
>>      No default Proper Dih. types
>>
>> ERROR 6 [file topol.top, line 3278]:
>>      No default Improper Dih. types
> All this probably follows on from the confused state of bonding to H1,
> e.g. if CN-H1 is defined from the .rtp bond, and there's now a C-H1 from
> the possibly erroneous .hdb construction. What is line 414 of topol.top?
>
> * line 414 of topol.tp:
>      [bonds]
>         1     2     1

That's what it is in the new version, not the old version that actually 
had the errors.

What does grompp have to say now?

Mark
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