[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 14 11:56:13 CEST 2008
vivek sharma wrote:
> Hi Justin,
> Thanx for your helpful advice, but i have corrected the name of 2nd 3rd
> molecule as shown in last mail, still it is showing errors can you
> suggest some good tutorial for understanding the nomenclature for atoms
> in those files (My apologies for asking you something out of the topic)
>
The best reading is the Gromacs manual. If you are still getting the same
error, it simply means you haven't re-named everything appropriately and you
need to carefully check your work.
-Justin
> With Thanx,
> Vivek
>
> 2008/8/13 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
> Every atom must be named appropriately, not just the first. Keep
> making the appropriate changes.
>
> -Justin
>
> vivek sharma wrote:
>
> Hi Justin,
> Thanx again, your option worked for me now it is giving error
> for the atom just next to PA (changed to AP) i.e. AO1 as
>
> Processing chain 5 'E' (372 atoms, 9 residues)
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.3
> Source code file: pdb2gmx.c, line: 421
>
> Fatal error:
> Atom AO1 in residue NDPH 1 not found in rtp entry with 56 atoms
> while sorting atoms
> -------------------------------------------------------
> following is the ligand atoms from the .rtp file
>
> [ NADH ]
> [ atoms ]
> AP P 0.76000 0
> AO1P OM -0.63500 0
> AO2P OM -0.63500 0
> AO5* OA -0.36000 0
> O3P OA -0.26000 1
> NP P 0.76000 1
> NO1P OM -0.63500 1
> NO2P OM -0.63500 1
> NO5* OA -0.36000 1
> AC5* CH2 0.00000 2
> AC4* CH1 0.16000 3
> AO4* OA -0.36000 3
> AC1* CH1 0.20000 3
> AN9 NR -0.20000 4
> AC4 C 0.20000 4
> AN3 NR -0.36000 5
> AC2 CR1 0.36000 5
> AN1 NR -0.36000 6
> AC6 C 0.36000 6
> AN6 NT -0.83000 7
> AH61 H 0.41500 7
> AH62 H 0.41500 7
> AC5 C 0.00000 8
> AN7 NR -0.36000 8
> AC8 CR1 0.36000 8
> AC2* CH1 0.15000 9
> AO2* OA -0.54800 9
> AH2* H 0.39800 9
> AC3* CH1 0.15000 10
> AO3* OA -0.54800 10
> AH3* H 0.39800 10
> NC5* CH2 0.00000 11
> NC4* CH1 0.16000 12
> NO4* OA -0.36000 12
> NC1* CH1 0.20000 12
> NN1 NR -0.20000 13
> NC6 CR1 0.20000 13
> NC2 CR1 0.00000 13
> NC3 C 0.00000 13
> NC4 CH2 0.00000 13
> NC5 CR1 0.00000 13
> NC7 C 0.38000 14
> NO7 O -0.38000 14
> NN7 NT -0.83000 15
> NH71 H 0.41500 15
> NH72 H 0.41500 15
> NC2* CH1 0.15000 16
> NO2* OA -0.54800 16
> NH2* H 0.39800 16
> NC3* CH1 0.15000 17
> NO3* OA -0.54800 17
> NH3* H 0.39800 17
>
> And the corresponding atom listing from 1XU9.pdb is as...
>
> HETATM 8111 AP NDPH 1 8.809 -4.754 22.676 1.00 12.71
> HETATM 8112 AO1 NDPH 1 10.106 -4.137 23.158 1.00 11.98
> HETATM 8113 AO2 NDPH 1 8.869 -5.751 21.580 1.00 13.09
> HETATM 8114 O5B NDPH 1 8.010 -5.348 23.937 1.00 12.91
> HETATM 8115 C5B NDPH 1 6.913 -6.239 23.752 1.00 12.91
> HETATM 8116 C4B NDPH 1 6.493 -6.754 25.120 1.00 10.44
> HETATM 8117 O4B NDPH 1 5.292 -7.535 24.969 1.00 13.02
> HETATM 8118 C3B NDPH 1 7.588 -7.667 25.612 1.00 10.90
> HETATM 8119 O3B NDPH 1 7.552 -7.543 27.047 1.00 12.99
> HETATM 8120 C2B NDPH 1 7.086 -9.053 25.407 1.00 12.38
> HETATM 8121 O2B NDPH 1 7.660 -10.046 26.246 1.00 13.11
> HETATM 8122 C1B NDPH 1 5.579 -8.877 25.356 1.00 12.53
> HETATM 8123 N9A NDPH 1 4.817 -9.905 24.673 1.00 11.65
> HETATM 8124 C8A NDPH 1 5.033 -10.388 23.429 1.00 10.38
> HETATM 8125 N7A NDPH 1 4.132 -11.360 23.119 1.00 11.50
> HETATM 8126 C5A NDPH 1 3.332 -11.498 24.179 1.00 10.26
> HETATM 8127 C6A NDPH 1 2.217 -12.337 24.568 1.00 11.19
> HETATM 8128 N6A NDPH 1 1.746 -13.251 23.689 1.00 12.10
> HETATM 8129 N1A NDPH 1 1.678 -12.169 25.805 1.00 11.24
> HETATM 8130 C2A NDPH 1 2.130 -11.262 26.690 1.00 10.83
> HETATM 8131 N3A NDPH 1 3.161 -10.439 26.428 1.00 10.06
> HETATM 8132 C4A NDPH 1 3.776 -10.558 25.154 1.00 11.15
> HETATM 8133 O3 NDPH 1 7.769 -3.631 22.173 1.00 12.62
> HETATM 8134 PN NDPH 1 7.989 -2.036 22.130 1.00 12.08
> HETATM 8135 O1N NDPH 1 8.430 -1.526 23.461 1.00 11.89
> HETATM 8136 O2N NDPH 1 8.741 -1.692 20.889 1.00 11.73
> HETATM 8137 O5D NDPH 1 6.467 -1.533 21.886 1.00 12.66
> HETATM 8138 C5D NDPH 1 5.611 -1.361 23.020 1.00 11.65
> HETATM 8139 C4D NDPH 1 4.298 -0.748 22.582 1.00 11.67
> HETATM 8140 O4D NDPH 1 4.556 0.487 21.875 1.00 12.21
> HETATM 8141 C3D NDPH 1 3.548 -1.649 21.637 1.00 11.97
> HETATM 8142 O3D NDPH 1 2.175 -1.497 22.010 1.00 11.22
> HETATM 8143 C2D NDPH 1 3.579 -0.984 20.290 1.00 12.02
> HETATM 8144 O2D NDPH 1 2.475 -1.229 19.433 1.00 11.31
> HETATM 8145 C1D NDPH 1 3.974 0.454 20.593 1.00 12.46
> HETATM 8146 N1N NDPH 1 4.714 1.092 19.529 1.00 11.43
> HETATM 8147 C2N NDPH 1 6.045 0.998 19.502 1.00 11.26
> HETATM 8148 C3N NDPH 1 6.724 1.599 18.453 1.00 10.05
> HETATM 8149 C7N NDPH 1 8.217 1.540 18.362 1.00 11.67
> HETATM 8150 O7N NDPH 1 8.756 2.105 17.403 1.00 11.17
> HETATM 8151 N7N NDPH 1 8.916 0.848 19.266 1.00 11.33
> HETATM 8152 C4N NDPH 1 6.022 2.270 17.471 1.00 10.99
> HETATM 8153 C5N NDPH 1 4.641 2.345 17.528 1.00 11.46
> HETATM 8154 C6N NDPH 1 4.005 1.748 18.602 1.00 12.11
> HETATM 8155 P2B NDPH 1 7.584 -11.626 25.952 1.00 13.18
> HETATM 8156 O1X NDPH 1 8.540 -12.200 26.975 1.00 15.49
> HETATM 8157 O2X NDPH 1 6.162 -12.049 26.180 1.00 13.31
> HETATM 8158 O3X NDPH 1 8.073 -11.835 24.534 1.00 13.10
> HETATM 8159 PA NDPH 2 -29.029 -5.471 7.894 1.00 12.85
> HETATM 8160 O1A NDPH 2 -30.208 -4.995 7.102 1.00 13.51
> HETATM 8161 O2A NDPH 2 -29.200 -5.823 9.322 1.00 11.99
> HETATM 8162 O5B NDPH 2 -28.355 -6.688 7.107 1.00 11.99
> HETATM 8163 C5B NDPH 2 -27.299 -7.469 7.665 1.00 12.75
> HETATM 8164 C4B NDPH 2 -27.105 -8.686 6.774 1.00 11.47
>
> now trick is not working for atom next to PA, please tell me if
> there is any thing should be taken care while doing so.
> sorry for cribbing you again and again, but I am helpless in
> this field.
> Please suggest
>
> With Thanx,
> Vivek
>
> 2008/8/13 Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>>
>
>
>
>
> vivek sharma wrote:
>
> Hi Justin,
> Thanx for your suggestion. But, I am not getting how to do
> correction in those files I am using gromacs 3.3.3 and
> 1XU9.pdb
> molecule for my simulation.
> I am not getting what is happening in the
> simulation...:(...:(
> kindly suggest.
>
>
> I'm guessing that NDP is the NADPH cofactor, which in Gromos96
> language is called NDPH (that's what pdb2gmx is trying to
> call, it
> as well). What's happening is you've got the atoms present for
> NADPH, but the force field simply has different names for the
> atoms.
>
> The simple fix is to re-name the atoms in the .pdb file
> according to
> how they appear in the .rtp entry for NADPH (called NDPH). For
> example, the two phosphorus atoms in the phosphodiester
> between the
> adenosine and nicotinamide moieties are called AP and NP. AP
> corresponds to the P atom in the phosphate donated by the
> adenoside
> system; NP corresponds to the P atom from the nicotinamide
> phosphate. You've got an atom called PA instead, which is
> probably
> equivalent to AP (but do check, because that's just a guess
> from my
> end).
>
> -Justin
>
>
> With Thanx,
> Vivek
>
>
> 2008/8/13 Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>
>
>
> There are two potential solutions to this error. For
> background,
> refer to:
>
>
> http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
>
> So your options are:
>
> 1. If the ligand is present in the .rtp file, make
> sure your atom
> nomenclature corresponds to that of the force field.
> 2. Remove the ligand and deal with its topology separately
> (search
> Google for John Kerrigan's tutorial for enzyme-ligand
> systems).
>
> -Justin
>
> vivek sharma wrote:
>
> Hi Nahren,
> Thanx for your help, I opened the pdb file with
> swisspdb
> viewer
> and then tried the pdb2gmx command over that pdb
> file and got
> the following error.
>
> Total mass 28295.072 a.m.u.
> Total charge 1.000 e
> Writing topology
> Processing chain 5 'E' (372 atoms, 9 residues)
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Warning: 'NDP' not found in residue topology database,
> trying to
> use 'NDPH'
>
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.3
> Source code file: pdb2gmx.c, line: 421
>
> Fatal error:
> Atom PA in residue NDPH 1 not found in rtp entry
> with 56
> atoms
> while sorting atoms
>
> -------------------------------------------------------
>
> and the error for the all atom forcefield were as
> follow.
>
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.3
> Source code file: resall.c, line: 436
>
> Fatal error:
> Residue 'NDP' not found in residue topology database
>
>
> -------------------------------------------------------
> any advice for this will be of great help
> for me.
>
> Thanx,
> Vivek
>
> 2008/8/12 nahren manuel <meetnahren at yahoo.com
> <mailto:meetnahren at yahoo.com>
> <mailto:meetnahren at yahoo.com <mailto:meetnahren at yahoo.com>>
> <mailto:meetnahren at yahoo.com
> <mailto:meetnahren at yahoo.com>
> <mailto:meetnahren at yahoo.com
> <mailto:meetnahren at yahoo.com>>> <mailto:meetnahren at yahoo.com
> <mailto:meetnahren at yahoo.com>
> <mailto:meetnahren at yahoo.com <mailto:meetnahren at yahoo.com>>
>
> <mailto:meetnahren at yahoo.com
> <mailto:meetnahren at yahoo.com> <mailto:meetnahren at yahoo.com
> <mailto:meetnahren at yahoo.com>>>>>
>
>
>
> Dear Vivek,
> you just have to download swisspdb and open
> your pdb file.
> Thats all
> you got to do and It is more than enough. If
> you have more
> than 2/3
> residues missing then, make sure the Ramachandran
> plots are fine.
> Also try a simple minimization before begining
> gromacs.
> nahren
>
> --- On *Tue, 8/12/08, vivek sharma
> /<viveksharma.iitb at gmail.com
> <mailto:viveksharma.iitb at gmail.com>
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> <mailto:viveksharma.iitb at gmail.com>
> <mailto:viveksharma.iitb at gmail.com
> <mailto:viveksharma.iitb at gmail.com>>>
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> <mailto:viveksharma.iitb at gmail.com>>>>>/* wrote:
>
> From: vivek sharma
> <viveksharma.iitb at gmail.com <mailto:viveksharma.iitb at gmail.com>
> <mailto:viveksharma.iitb at gmail.com
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>
> Subject: Re: [gmx-users] Error in
> pdb2gmx.....Atom CE2
> not found
> in residue PHE270 while adding hydrogens
> To: "Discussion list for GROMACS users"
> <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
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>
> Date: Tuesday, August 12, 2008, 6:34 PM
>
>
> Hi David,
> Thanx a lot again. can you please tell me the
> criteria or the
> standards to do such correction or can you
> suggest
> some
> link or
> tutorial for the same?
> whether swiss pdb can help in such cases?
>
> With Thanx,
> Vivek
>
>
>
> 2008/8/12 David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
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> <mailto:spoel at xray.bmc.uu.se>>>
> <mailto:spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> <mailto:spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>>>>>
>
>
>
> vivek sharma wrote:
>
> Hi There,
>
> I am new to molecular dynamics and
> GROMACS.
> While trying MD for 1XU9.pdb (pdbid) in
> the very 1st
> step on using the command....
>
> pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p
> 1XU9.top -i
> 1XU9.itp
> -vsite hydrogen -water spce
>
> I got the following in the last of
> error.....
> ......
> ......
> ......
> .......
> N-terminus: NH3+
> C-terminus: COO-
> WARNING: atom CE2 not found in
> residue 270
> while
> adding atom
>
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.3
> Source code file: genhydro.c, line: 304
>
> Fatal error:
> Atom CE2 not found in residue
> PHE270 while
> adding
> hydrogens
>
> -------------------------------------------------------
> I tried the same with different force
> field and
> water
> models, but getting the same error
> again
> and again.
> any suggestion will be highly
> appreciated.
>
>
> You have an incorrect pdb file. An atom is
> missing.
> You have
> to fix it yourself.
>
>
>
> With thanx,
> Vivek
>
>
> ------------------------------------------------------------------------
>
>
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> -- ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
> <http://vt.edu> | (540)
>
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
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>
> -- ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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