[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
vivek sharma
viveksharma.iitb at gmail.com
Wed Aug 13 10:37:23 CEST 2008
Hi There,
For the error I mentioned in last mail I looked in the .rtp file and .pdb
file for residue NDP. Following is the part of .pdb file showing atoms as
PA, O1A etc
HETATM 8111 PA NDP 1 8.809 -4.754 22.676 1.00 12.71
HETATM 8112 O1A NDP 1 10.106 -4.137 23.158 1.00 11.98
HETATM 8113 O2A NDP 1 8.869 -5.751 21.580 1.00 13.09
HETATM 8114 O5B NDP 1 8.010 -5.348 23.937 1.00 12.91
HETATM 8115 C5B NDP 1 6.913 -6.239 23.752 1.00 12.91
HETATM 8116 C4B NDP 1 6.493 -6.754 25.120 1.00 10.44
HETATM 8117 O4B NDP 1 5.292 -7.535 24.969 1.00 13.02
HETATM 8118 C3B NDP 1 7.588 -7.667 25.612 1.00 10.90
HETATM 8119 O3B NDP 1 7.552 -7.543 27.047 1.00 12.99
HETATM 8120 C2B NDP 1 7.086 -9.053 25.407 1.00 12.38
HETATM 8121 O2B NDP 1 7.660 -10.046 26.246 1.00 13.11
HETATM 8122 C1B NDP 1 5.579 -8.877 25.356 1.00 12.53
HETATM 8123 N9A NDP 1 4.817 -9.905 24.673 1.00 11.65
HETATM 8124 C8A NDP 1 5.033 -10.388 23.429 1.00 10.38
HETATM 8125 N7A NDP 1 4.132 -11.360 23.119 1.00 11.50
HETATM 8126 C5A NDP 1 3.332 -11.498 24.179 1.00 10.26
HETATM 8127 C6A NDP 1 2.217 -12.337 24.568 1.00 11.19
HETATM 8128 N6A NDP 1 1.746 -13.251 23.689 1.00 12.10
HETATM 8129 N1A NDP 1 1.678 -12.169 25.805 1.00 11.24
HETATM 8130 C2A NDP 1 2.130 -11.262 26.690 1.00 10.83
HETATM 8131 N3A NDP 1 3.161 -10.439 26.428 1.00 10.06
HETATM 8132 C4A NDP 1 3.776 -10.558 25.154 1.00 11.15
HETATM 8133 O3 NDP 1 7.769 -3.631 22.173 1.00 12.62
HETATM 8134 PN NDP 1 7.989 -2.036 22.130 1.00 12.08
HETATM 8135 O1N NDP 1 8.430 -1.526 23.461 1.00 11.89
HETATM 8136 O2N NDP 1 8.741 -1.692 20.889 1.00 11.73
HETATM 8137 O5D NDP 1 6.467 -1.533 21.886 1.00 12.66
HETATM 8138 C5D NDP 1 5.611 -1.361 23.020 1.00 11.65
HETATM 8139 C4D NDP 1 4.298 -0.748 22.582 1.00 11.67
HETATM 8140 O4D NDP 1 4.556 0.487 21.875 1.00 12.21
HETATM 8141 C3D NDP 1 3.548 -1.649 21.637 1.00 11.97
HETATM 8142 O3D NDP 1 2.175 -1.497 22.010 1.00 11.22
HETATM 8143 C2D NDP 1 3.579 -0.984 20.290 1.00 12.02
HETATM 8144 O2D NDP 1 2.475 -1.229 19.433 1.00 11.31
HETATM 8145 C1D NDP 1 3.974 0.454 20.593 1.00 12.46
HETATM 8146 N1N NDP 1 4.714 1.092 19.529 1.00 11.43
HETATM 8147 C2N NDP 1 6.045 0.998 19.502 1.00 11.26
HETATM 8148 C3N NDP 1 6.724 1.599 18.453 1.00 10.05
HETATM 8149 C7N NDP 1 8.217 1.540 18.362 1.00 11.67
HETATM 8150 O7N NDP 1 8.756 2.105 17.403 1.00 11.17
HETATM 8151 N7N NDP 1 8.916 0.848 19.266 1.00 11.33
HETATM 8152 C4N NDP 1 6.022 2.270 17.471 1.00 10.99
HETATM 8153 C5N NDP 1 4.641 2.345 17.528 1.00 11.46
HETATM 8154 C6N NDP 1 4.005 1.748 18.602 1.00 12.11
HETATM 8155 P2B NDP 1 7.584 -11.626 25.952 1.00 13.18
HETATM 8156 O1X NDP 1 8.540 -12.200 26.975 1.00 15.49
HETATM 8157 O2X NDP 1 6.162 -12.049 26.180 1.00 13.31
HETATM 8158 O3X NDP 1 8.073 -11.835 24.534 1.00 13.10
......and following is the part of .rtp file for details of residue NDP
[ NDPH ]
[ 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 -0.36000 9
AP2* P 0.63000 9
AO6* OM -0.63500 9
AO7* OM -0.63500 9
AO8* OA -0.54800 9
AH8* 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
are those file indicating some error like atom name are different in two
files, is this the reason for my error or I have to think in some other way.
Any advice would be of great help.
With Thanx,
Vivek
2008/8/13 vivek sharma <viveksharma.iitb at gmail.com>
> 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>
>
> 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>* wrote:
>>
>> From: vivek sharma <viveksharma.iitb at gmail.com>
>> 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>
>> 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>
>>
>>> 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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>>>
>>>
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