[gmx-users] pdb2gmx picks up the wrong .tdb files?
András Ferenc WACHA
wacha.andras at ttk.hu
Thu Jan 16 16:07:56 CET 2020
Dear Justin,
thank you. Am I doing something wrong or is this a bug in Gromacs? Do
you have a suggestion how to make this work? Should I rename the
terminal patches or should I put everything under one basename
(sacrificing cleanliness and maintainability)?
Kind regards,
Andras
On 1/16/20 2:47 PM, Justin Lemkul wrote:
>
>
> On 1/16/20 8:44 AM, András Ferenc WACHA wrote:
>> Sorry, now replying to the whole list:
>>
>> Dear Justin,
>>
>> I have obtained the base force field from the website of the MacKerell
>> Lab
>> (http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz).
>> I have checked and the merged.n.tdb file is the same in my version and
>> in theirs.
>>
>> Shouldn't pdb2gmx only use the termini databases corresponding to the
>> .rtp file from which the given residue has been read? I.e. if it is LYS,
>> found in merged.rtp, then only merged.{n,c}.tdb?
>
> The base names should match between .rtp and .tdb but I have never
> tried having multiple types of protein residues in different files.
>
> -Justin
>
>> Kind regards,
>>
>> Andras
>>
>> On 1/16/20 2:33 PM, Justin Lemkul wrote:
>>> On 1/16/20 8:04 AM, András Ferenc WACHA wrote:
>>>> Dear fellow Gromacs users,
>>>>
>>>> I have developed an extended version of the CHARMM36m force field for
>>>> beta-amino acids (https://charmm-betaff.readthedocs.io,
>>>> https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found
>>>> pdb2gmx works well. However, if I try to use it for natural peptides and
>>>> proteins (e.g. 6LYZ from the PDB), the following command:
>>>>
>>>> gmx pdb2gmx -f 6LYZ.pdb, -ff charmm-beta -ter -ignh
>>>>
>>>> fails to recognize the correct termini database files. The output is the
>>>> following:
>>>>
>>>> (-------------------------- START of gmx output
>>>> -----------------------------------)
>>>>
>>>> GROMACS: gmx pdb2gmx, version 2020
>>>> Executable:
>>>> /opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir/bin/gmx
>>>>
>>>> Data prefix:
>>>> /opt/spack/opt/spack/linux-archrolling-skylake/gcc-9.2.0/gromacs-2020-ls53yrft6droj2ovhuzdwdufi4an4vir
>>>>
>>>> Working dir: /home/wachaandras/gromacs/forcefields
>>>> Command line:
>>>> gmx pdb2gmx -f 6lyz.pdb -ff charmm-beta -ter -ignh
>>>>
>>>> Using the Charmm-beta force field in directory ./charmm-beta.ff
>>>>
>>>> Opening force field file ./charmm-beta.ff/watermodels.dat
>>>>
>>>> Select the Water Model:
>>>> 1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with
>>>> LJ on H
>>>> 2: TIP4P TIP 4-point
>>>> 3: TIP5P TIP 5-point
>>>> 4: SPC simple point charge
>>>> 5: SPC/E extended simple point charge
>>>> 6: Methanol Equilibrated methanol
>>>> 7: Octanol Equilibrated octanol
>>>> 8: None
>>>> 1
>>>> going to rename ./charmm-beta.ff/merged.r2b
>>>> Opening force field file ./charmm-beta.ff/merged.r2b
>>>> Reading 6lyz.pdb...
>>>> WARNING: all CONECT records are ignored
>>>> Read '', 1001 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 129 residues with 1001
>>>> atoms
>>>>
>>>> chain #res #atoms
>>>> 1 'A' 129 1001
>>>>
>>>> All occupancies are one
>>>> Opening force field file ./charmm-beta.ff/atomtypes.atp
>>>> Opening force field file ./charmm-beta.ff/betaaminoacids.atp
>>>> Opening force field file ./charmm-beta.ff/cyclicbeta.atp
>>>> Reading residue database... (Charmm-beta)
>>>> Opening force field file ./charmm-beta.ff/betaaminoacids.rtp
>>>> Opening force field file ./charmm-beta.ff/cyclicbeta.rtp
>>>> Opening force field file ./charmm-beta.ff/extra.rtp
>>>> Warning: file does not end with a newline, last line:
>>>> ;
>>>> Opening force field file ./charmm-beta.ff/merged.rtp
>>>> Opening force field file ./charmm-beta.ff/merged.hdb
>>>> Opening force field file ./charmm-beta.ff/betaaminoacids.n.tdb
>>>> Opening force field file ./charmm-beta.ff/cyclicbeta.n.tdb
>>>> Opening force field file ./charmm-beta.ff/merged.n.tdb
>>>> Opening force field file ./charmm-beta.ff/betaaminoacids.c.tdb
>>>> Opening force field file ./charmm-beta.ff/cyclicbeta.c.tdb
>>>> Opening force field file ./charmm-beta.ff/merged.c.tdb
>>>> Processing chain 1 'A' (1001 atoms, 129 residues)
>>>> Analysing hydrogen-bonding network for automated assignment of histidine
>>>> protonation. 213 donors and 184 acceptors were found.
>>>> There are 262 hydrogen bonds
>>>> Will use HISD for residue 15
>>>> Identified residue LYS1 as a starting terminus.
>>>> Identified residue LEU129 as a ending terminus.
>>>> 8 out of 8 lines of specbond.dat converted successfully
>>>> Special Atom Distance matrix:
>>>> CYS6 MET12 HIS15 CYS30 CYS64 CYS76
>>>> CYS80
>>>> SG48 SD87 NE2118 SG238 SG513 SG601
>>>> SG630
>>>> MET12 SD87 1.205
>>>> HIS15 NE2118 1.804 0.998
>>>> CYS30 SG238 1.450 1.070 2.063
>>>> CYS64 SG513 2.873 1.779 1.755 2.236
>>>> CYS76 SG601 2.740 1.544 1.418 2.132 0.778
>>>> CYS80 SG630 3.006 1.943 1.892 2.387 0.200 0.958
>>>> CYS94 SG724 2.576 1.388 1.329 1.976 0.678 0.211
>>>> 0.871
>>>> MET105 SD799 1.866 0.933 1.679 0.896 1.858 1.483
>>>> 2.047
>>>> CYS115 SG889 1.625 1.099 2.068 0.204 2.108 2.005
>>>> 2.260
>>>> CYS127 SG981 0.203 1.089 1.733 1.332 2.808 2.631
>>>> 2.950
>>>> CYS94 MET105 CYS115
>>>> SG724 SD799 SG889
>>>> MET105 SD799 1.389
>>>> CYS115 SG889 1.855 0.790
>>>> CYS127 SG981 2.474 1.701 1.505
>>>> Linking CYS-6 SG-48 and CYS-127 SG-981...
>>>> Linking CYS-30 SG-238 and CYS-115 SG-889...
>>>> Linking CYS-64 SG-513 and CYS-80 SG-630...
>>>> Linking CYS-76 SG-601 and CYS-94 SG-724...
>>>> Select start terminus type for LYS-1
>>>> 0: Beta3NH3+
>>>> 1: Beta2NH3+
>>>> 2: Beta23NH3+
>>>> 3: B3_NH2
>>>> 4: B2_NH2
>>>> 5: B23_NH2
>>>> 6: 5TER
>>>> 7: None
>>>>
>>>> (-------------------------- END of gmx output
>>>> -----------------------------------)
>>>>
>>>> Information in the force field relevant to the beta-peptides is stored
>>>> in betaaminoacids.{arn,atp,c.tdb,n.tdb,rtp} files. I have kept the
>>>> original ones (merged.*) intact. From the output above it seems that
>>>> pdb2gmx recognizes and loads all the relevant files (both
>>>> betaaminoacids.* and merged.*), but only shows a selection of N-terminal
>>>> patches from the betaaminoacids.n.tdb file. More precisely, the 5TER
>>>> terminus is from merged.n.tdb, but the other ones before it get
>>>> overridden by entries from betaaminoacids.n.tdb. Is there some rule in
>>>> pdb2gmx which considers some endgroups equivalent and keeps only one? I
>>>> have encountered it neither in the main documentation (section 5.6.5:
>>>> pdb2gmx input files), nor in the help of gmx pdb2gmx.
>>>>
>>>> Could anyone point me to how I should do this correctly?
>>> What is the source of these force field files? Based on the .tdb
>>> entries, it seems they do not include the "standard" patches that
>>> should be included with the official CHARMM force field.
>>>
>>> -Justin
>>>
>>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
--
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible
Biological Nanochemistry Research Group (310)
Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences (RCNS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.hu
CREDO SAXS instrument: http://credo.ttk.hu
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