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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