[gmx-users] Problem fpr building a peptide with two modified residues with amber ff
ABEL Stephane
Stephane.ABEL at cea.fr
Sun Jan 14 16:52:36 CET 2018
----------------------------------------------------------
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
________________________________________
De : ABEL Stephane
Envoyé : dimanche 14 janvier 2018 16:52
À : 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.
Stéphane
------------------------------
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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