Re: [gmx-users] Fix the residues

[Amir Zeb]

Is TYR and SER are N-terminal and C-terminal residues , respectively?
Also, you may compare the corresponding atoms of each residues with same
residues present in your system and does not show the mentioned warning.

All the best

On Fri, Jan 6, 2017 at 10:58 AM, liming_52  wrote:

> Dear Gromacs users,
>
> I am trying to run a md using 4n6p.cif, which was obtained from PDB. I
> converted the file into pdb format using DS4.1, and got the file named
> lactoferrin.pdb. When I directly run
> the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water
> spce", the program runs and produces the information as follows:
> ...
> WARNING: WARNING: Residue 1 named TYR of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> WARNING: WARNING: Residue 335 named SER of a molecule in the input file
> was mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> ...
> How should I fix the residues? And which tools should I use? Is there any
> examples or tutorials?
>
> If anyone can suggest a solution to this issue, it would be really helpful.
>
>
>
>
>
>
>
> --
>
> With my best wishes,
> Ming Li, PhD
> Chinese Academy of Agricultural Sciences, Beijing, China
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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>
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Re: [gmx-users] Fix the residues

[Justin Lemkul]

On 1/6/17 2:41 PM, liming_52 wrote:

Thank you for reppy. The full information is as follows:
$ gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce
  :-) GROMACS - gmx pdb2gmx, VERSION 5.1.4 (-:
GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner
Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS:  gmx pdb2gmx, VERSION 5.1.4
Executable:   /usr/local/gromacs/bin//gmx.exe
Data prefix:  /usr/local/gromacs
Command line:
  gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce

Select the Force Field:
From '/usr/local/gromacs/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
9
Using the Gromos43a1 force field in directory gromos43a1.ff
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.r2b
Reading lactoferrin.pdb...
WARNING: all CONECT records are ignored
Read 2560 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 335 residues with 2560 atoms
  chain  #res #atoms
  1 'A'   335   2560
All occupancies are one
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/atomtypes.atp
Atomtype 50
Reading residue database... (gromos43a1)
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.rtp
Residue 96
Sorting it all out...
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.hdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 'A' (2560 atoms, 335 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 500 donors and 499 acceptors were found.
There are 743 hydrogen bonds
Will use HISE for residue 420
Will use HISH for residue 458
Will use HISD for residue 588
Will use HISE for residue 595
Will use HISE for residue 606
Will use HISE for residue 613
Identified residue TYR342 as a starting terminus.
Identified residue SER676 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
  CYS348  CYS358  CYS371  CYS380  CYS405  HIS420  CYS425
SG64   SG138   SG241   SG300   SG481  NE2595   SG629
  CYS358   SG138   0.849
  CYS371   SG241   0.940   0.213
  CYS380   SG300   0.204   0.933   1.049
  CYS405   SG481   1.411   2.186   2.303   1.371
  HIS420  NE2595   3.406   3.321   3.509   3.348   3.338
  CYS425   SG629   2.460   2.150   2.323   2.429   2.901   1.313
  CYS457   SG875   2.702   2.932   3.096   2.502   2.930   3.532   3.094
  

Re: [gmx-users] Fix the residues

[Justin Lemkul]

On 1/6/17 1:58 PM, liming_52 wrote:

Dear Gromacs users,

I am trying to run a md using 4n6p.cif, which was obtained from PDB. I 
converted the file into pdb format using DS4.1, and got the file named 
lactoferrin.pdb. When I directly run
the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce", 
the program runs and produces the information as follows:
...


You snipped out the most important information.  Please provide the full screen 
output from pdb2gmx.


-Justin


WARNING: WARNING: Residue 1 named TYR of a molecule in the input file was mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 335 named SER of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

...
How should I fix the residues? And which tools should I use? Is there any 
examples or tutorials?

If anyone can suggest a solution to this issue, it would be really helpful.







--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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[gmx-users] Fix the residues

[liming_52]

Dear Gromacs users,

I am trying to run a md using 4n6p.cif, which was obtained from PDB. I 
converted the file into pdb format using DS4.1, and got the file named 
lactoferrin.pdb. When I directly run
the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce", 
the program runs and produces the information as follows:
...
WARNING: WARNING: Residue 1 named TYR of a molecule in the input file was mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
 
WARNING: WARNING: Residue 335 named SER of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

...
How should I fix the residues? And which tools should I use? Is there any 
examples or tutorials?

If anyone can suggest a solution to this issue, it would be really helpful.







--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.