[gmx-users] Diagnosing + system blowing up
Shima Arasteh
shima_arasteh2001 at yahoo.com
Tue Jul 31 23:41:51 CEST 2012
All right. Thanks.
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc:
Sent: Wednesday, August 1, 2012 2:04 AM
Subject: Re: [gmx-users] Diagnosing + system blowing up
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_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
>
--
========================================
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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