[gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

ABEL Stephane Stephane.ABEL at cea.fr
Mon Jan 15 18:31:54 CET 2018


Hello, 

I have finally resolved my problem thank to Justin . 

Bye 
------------------------------

Message: 2
Date: Sun, 14 Jan 2018 17:36:21 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
        modified residues with amber ff
Message-ID: <b7a10948-61d2-5b3f-b062-6630785c61af at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 12:04 PM, ABEL Stephane wrote:
> Thank you, Justin for your interest to my problem,
>
> But even if I use the -missing argument*, pdb2gmx still wants to add an Nter ILE instead of a central a simple ILE :((

Ile should not be treated as a terminal residue, and it wasn't in the
screen output you provided before after adding your custom residues to
residuetypes.dat. That's a prerequisite if you want anything to work.
Getting the connectivity right after dealing with the custom residues is
the next problem after that.

-Justin

> *gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o Atosiban_amber14sb.pdb -i Atosiban_posre.itp -missing
>
> I will try to search a workaround
>
> Best
>
> St?phane
>
> ________________________________________
> De : ABEL Stephane
> Envoy? : dimanche 14 janvier 2018 16:52
> ? : gromacs.org_gmx-users at maillist.sys.kth.se
> Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50
>
> Thanks Justin
>
> First I forgot to say that I am building a cyclic peptide (Atosiban, https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER (3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the two residues are well constructed and linked together with pdb2gmx as it is shown If I consider the ILE as NILE
>
> For linking the MER and CYX I define a bond with the specbond.dat (the corresponding bond is shown in the  pdb2gmx output). The only problem I have is that NILE residue is chosen instead of ILE
>
> How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or I found a subtle error I cannot find.
>
> St?phane
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 14 Jan 2018 10:34:08 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem fpr building a peptide with two
>          modified residues with amber ff
> Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4d22 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/14/18 10:04 AM, ABEL Stephane wrote:
>> Hi Justin
>>
>> I have added the TYO and MER residue as Protein is the residuetypes.dat. And the the following output with pdb2gmx. I select 2 and 6
>>
>> ##########
>>     gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes
>>
>>
>> Select the Force Field:
>>   From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
>>    1: Amber12sb ff99SB + new backbone and side chain torsion for protein
>>    2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
>>    3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
>>    4: CHARMM36 all-atom force field (July 2017)
>>    5: CHARMM36 all-atom force field, surfactants and pigments
>>    6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 2011, 115, 487-499 )
>>    7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 3825?3850)
>>    8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. Phys. Chem. C, 2015, 119 (14), pp 7888?7899)
>>    9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 10.1002/jcc.21675)
>> 10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
>>   From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
>> 11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
>> 12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>> 13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
>> 14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
>> 15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
>> 16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
>> 17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
>> 18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
>> 19: GROMOS96 43a1 force field
>> 20: GROMOS96 43a2 force field (improved alkane dihedrals)
>> 21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>> 22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>> 23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>> 24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
>> 25: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>> 2
>>
>> Using the Amber14sb_parmbsc1 force field in directory /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff
>>
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/watermodels.dat
>>
>> Select the Water Model:
>>    1: TIP3P     TIP 3-point, recommended
>>    2: TIP4P     TIP 4-point
>>    3: TIP4P-Ew  TIP 4-point optimized with Ewald
>>    4: SPC       simple point charge
>>    5: SPC/E     extended simple point charge
>>    6: None
>> 6
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.r2b
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.r2b
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.r2b
>> Reading Atosiban_box_ctr.pdb...
>> Read 'GROningen MAchine for Chemical Simulation', 85 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 10 residues with 85 atoms
>>
>>     chain  #res #atoms
>>     1 'A'    10     85
>>
>> All occupancies are one
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/atomtypes.atp
>> Atomtype 89Reading residue database... (amber14sb_parmbsc1)
>>
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/Merca.rtp
>> Residue 1
>> Sorting it all out...
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/TYO.rtp
>> Residue 2
>> Sorting it all out...
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.rtp
>> Residue 95
>> Sorting it all out...
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.rtp
>> Residue 111
>> Sorting it all out...
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.rtp
>> Residue 127
>> Sorting it all out...
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.hdb
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/dna.hdb
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/rna.hdb
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.n.tdb
>> Opening force field file /ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top//amber14sb_parmbsc1.ff/aminoacids.c.tdb
>>
>> Back Off! I just backed up Atosiban_amber14sb.top to ./#Atosiban_amber14sb.top.6#
>> Processing chain 1 'A' (85 atoms, 10 residues)
>> Identified residue MER1 as a starting terminus.
>> Identified residue NH210 as a ending terminus.
>> 1 out of 1 lines of specbond.dat converted successfully
>> Special Atom Distance matrix:
>>                       MER1
>>                        S11
>>       CYX6    SG63   0.200
>> Linking MER-1 S1-1 and CYX-6 SG-63...
>>
>> -------------------------------------------------------
>> Program gmx pdb2gmx, VERSION 5.1.2
>> Source code file: /tmp/gromacs/5.1.2/iomkl-156233.188/gromacs-5.1.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1083
>>
>> Fatal error:
>> There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Fix your terminal residues so that they match the residue database (.rtp) entries, or provide terminal database entries (.tdb).
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> ####
>>
>> Now indeed the MER and TYO as recognized as residues but I still obtain the dangling bond error
> The AMBER force fields are unique in that they do not support terminal
> group patching; your residue definitions for any terminal residues must
> be complete. I suspect your N-terminal MER residue does not have the
> proper -NH3+ terminus already built, so when pdb2gmx checks, it finds
> missing atoms. You need to specifically parametrize this residue in its
> terminal, not internal, form and supply that as your .rtp entry.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
>
> ------------------------------
>
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> End of gromacs.org_gmx-users Digest, Vol 165, Issue 50
> ******************************************************
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 14 Jan 2018 10:55:19 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue
>          50
> Message-ID: <d44769fa-da75-16f2-fbae-4ff815bb13c0 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/14/18 10:52 AM, ABEL Stephane wrote:
>> Thanks Justin
>>
>> First I forgot to say that I am building a cyclic peptide (Atosiban, https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER (3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the two residues are well constructed and linked together with pdb2gmx as it is shown If I consider the ILE as NILE
>>
>> For linking the MER and CYX I define a bond with the specbond.dat (the corresponding bond is shown in the  pdb2gmx output). The only problem I have is that NILE residue is chosen instead of ILE
>>
>> How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or I found a subtle error I cannot find.
> I've never dealt with cyclic peptides in GROMACS and most threads about
> them tend to die off without resolution. It's not something pdb2gmx does
> well. Presumably you could use the -missing flat (very dangerous!) and
> then verify that the topology has all the special bonds it needs.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>


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