[gmx-users] Diagnosing + system blowing up
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Jul 30 15:35:41 CEST 2012
On 30/07/2012 8:49 PM, Shima Arasteh wrote:
>
>
>> If you want further help, you will need to paste your .rtp entry(s), the N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full pdb2gmx output, the N-terminal fragment of the grompp -c input, grompp >command line, and full grompp output. You may think your context is clear, but nobody else is paying your problem as much attention as you are. I won't help further if you only provide partial information.
> 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 HG13grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr
>
> [ impropers ]
> CN N ON H1
>
> 2. hdb entry
In which file?
> 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
... and here's your .hdb file being picked up (and pdb2gmx must have
found definitions for building hydrogens for FVAL somehow)...
> 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.1#
> 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...
> Warning: Long Bond (1-18 = 0.357049 nm)
...but H1 is built as atom 18 and too far away...
> Number of bonds was 361, now 361
> Generating angles, dihedrals and pairs...
> Before cleaning: 920 pairs
> Before cleaning: 925 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...There are 22 cmap torsion pairs
> There are 925 dihedrals, 49 impropers, 642 angles
> 911 pairs, 361 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...
>
> --------- 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 3.040 1.903 2.415
> 1FVAL ON 2 3.028 2.024 2.435
> 1FVAL N 3 2.989 1.816 2.503
> 1FVAL HN 4 3.030 1.758 2.432
> 1FVAL CA 5 2.920 1.859 2.622
> 1FVAL HA 6 2.829 1.820 2.613
> 1FVAL CB 7 2.990 1.807 2.748
> 1FVAL HB 8 2.992 1.707 2.746
> 1FVAL CG1 9 3.133 1.861 2.752
> 1FVAL HG11 10 3.179 1.827 2.834
> 1FVAL HG12 11 3.182 1.830 2.671
> 1FVAL HG13 12 3.131 1.961 2.753
> 1FVAL CG2 13 2.914 1.855 2.871
> 1FVAL HG21 14 2.960 1.821 2.953
> 1FVAL HG22 15 2.912 1.955 2.873
> 1FVAL HG23 16 2.821 1.820 2.868
> 1FVAL C 17 2.915 2.011 2.631
> 1FVAL H1 18 2.825 2.031 2.670
... 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
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.
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 416]:
> No default Bond types
>
>
> ERROR 2 [file topol.top, line 1693]:
> No default U-B types
>
>
> ERROR 3 [file topol.top, line 1694]:
> No default U-B types
>
>
> ERROR 4 [file topol.top, line 2338]:
> No default Proper Dih. types
>
>
> ERROR 5 [file topol.top, line 3265]:
> 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 416 of topol.top?
Mark
>
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 1 [file topol.top, line 3365]:
> System has non-zero total charge: 1.000000
> Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> for discussion on how close it should be to an integer.
>
>
>
>
> There was 1 note
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/grompp.c, line: 1372
>
> Fatal error:
> There were 5 errors in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> I hope there are enough. If anything else, please let me know.
>
>
> Thanks,
> Shima
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