On 7/31/12 5:21 PM, Shima Arasteh wrote:
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.
You shouldn't delete lines from the topology. The errors indicate that the
interaction types you have defined do not exist in the force field. You need to
add suitable values, either by analogy to existing parameters or by a suitable
derivation protocol.
I would not trust any results from a topology that has been haphazardly modified
in this way. You may get rid of the grompp warnings, but you also get rid of
reliability.
-Justin
Sincerely,
Shima
________________________________
From: Shima Arasteh <shima_arasteh2...@yahoo.com>
To: Discussion list for GROMACS users <gmx-users@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.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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