[gmx-users] A query
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Feb 1 08:04:11 CET 2012
On 1/02/2012 4:19 PM, Anik Sen wrote:
> Hello,
> Am anik. Am using gromacs 4.5.5
>
> But the dna.rtp file contains the atom bname N3 under the residue file
> DT. So whats the problem then.
Yes, that's the reason from the problem. Your input structure doesn't
have that... I said:
> pdb2gmx can only match atom and residue names it finds in the topology
> database (.rtp). Your input structure lacks a (correctly named) N3
> atom in residue 31, which I think pdb2gmx looked for when building
> hydrogen atoms.
*Your input structure* doesn't match the .rtp. You need to change the
atom/residue naming of your input structure to conform.
Mark
>
> the dna.rtp file for DT
> [ DT ]
> [ atoms ]
> P P 1.16590 1
> O2 O1P -0.77610 2
> O2 O2P -0.77610 3
> OS O5' -0.49540 4
> CT C5' -0.00690 5
> H1 H5'1 0.07540 6
> H1 H5'2 0.07540 7
> CT C4' 0.16290 8
> H1 H4' 0.11760 9
> OS O4' -0.36910 10
> CT C1' 0.06800 11
> H2 H1' 0.18040 12
> N* N1 -0.02390 13
> CM C6 -0.22090 14
> H4 H6 0.26070 15
> CM C5 0.00250 16
> CT C7 -0.22690 17
> HC H71 0.07700 18
> HC H72 0.07700 19
> HC H73 0.07700 20
> C C4 0.51940 21
> O O4 -0.55630 22
> NA N3 -0.43400 23
> H H3 0.34200 24
> C C2 0.56770 25
> O O2 -0.58810 26
> CT C3' 0.07130 27
> H1 H3' 0.09850 28
> CT C2' -0.08540 29
> HC H2'1 0.07180 30
> HC H2'2 0.07180 31
> OS O3' -0.52320 32
>
> ------------------------------------------------------------------------
> *From:* gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org]
> on behalf of Mark Abraham [Mark.Abraham at anu.edu.au]
> *Sent:* Tuesday, January 31, 2012 7:09 PM
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] A query
>
> On 31/01/2012 9:04 PM, Anik Sen wrote:
>> Hello,
>> Am anik. Am using gromacs 4.5.5
>> I could not find the proper reason of the foillowig failure of my
>> job. please help.
>>
>> *The following is a part of the dna pdb file, which I am using:
>>
>> *ATOM 1 O5' DG5 X 1 13.663 36.760 21.465 0.00 0.00
>> ATOM 2 C1' DG5 X 1 14.791 36.040 21.150 0.00 0.00
>> ATOM 3 C4' DG5 X 1 14.771 34.703 21.873 0.00 0.00
>> ATOM 4 O4' DG5 X 1 16.017 34.553 22.577 0.00 0.00
>> ATOM 5 C5' DG5 X 1 13.724 34.528 22.970 0.00 0.00
>> ATOM 6 O3' DG5 X 1 13.540 33.118 23.234 0.00 0.00
>> ATOM 7 C3' DG5 X 1 14.362 35.323 24.108 0.00 0.00
>> ATOM 8 C2' DG5 X 1 15.856 35.044 23.903 0.00 0.00
>> ATOM 9 N1 DG5 X 1 16.753 36.193 24.040 0.00 0.00
>> ATOM 10 C8 DG5 X 1 16.484 37.562 24.004 0.00 0.00
>> ATOM 11 N7 DG5 X 1 17.551 38.308 24.156 0.00 0.00
>> ATOM 12 C4 DG5 X 1 18.589 37.359 24.268 0.00 0.00
>> ATOM 13 C6 DG5 X 1 19.989 37.514 24.448 0.00 0.00
>> ATOM 14 O6 DG5 X 1 20.648 38.553 24.534 0.00 0.00
>> ATOM 15 N9 DG5 X 1 20.645 36.287 24.525 0.00 0.00
>> ATOM 16 C2 DG5 X 1 20.048 35.045 24.439 0.00 0.00
>> ATOM 17 N3 DG5 X 1 20.848 33.965 24.540 0.00 0.00
>> ATOM 18 N5 DG5 X 1 18.753 34.884 24.262 0.00 0.00
>> ATOM 19 C5 DG5 X 1 18.095 36.074 24.193 0.00 0.00
>> ATOM 20 P DT X 2 12.650 32.528 24.445 0.00 0.00
>> ATOM 21 O1P DT X 2 12.016 31.284 23.943 0.00 0.00
>> ATOM 22 O2P DT X 2 11.806 33.610 25.015 0.00 0.00
>> ATOM 23 O5' DT X 2 13.743 32.102 25.531 0.00 0.00
>> ATOM 24 C3' DT X 2 14.653 31.088 25.184 0.00 0.00
>> ATOM 25 C2' DT X 2 15.813 31.114 26.126 0.00 0.00
>> ATOM 26 O3' DT X 2 16.429 32.408 26.092 0.00 0.00
>> ATOM 27 C5' DT X 2 15.420 30.906 27.570 0.00 0.00
>> ATOM 28 O4' DT X 2 15.818 29.609 27.955 0.00 0.00
>> ATOM 29 C4' DT X 2 16.171 31.996 28.340 0.00 0.00
>> ATOM 30 C1' DT X 2 17.115 32.536 27.293 0.00 0.00
>> ATOM 31 N3 DT X 2 17.425 33.937 27.428 0.00 0.00
>> ATOM 32 C2 DT X 2 18.741 34.313 27.581 0.00 0.00
>> ATOM 33 O2 DT X 2 19.667 33.515 27.649 0.00 0.00
>> ATOM 34 N1 DT X 2 18.932 35.671 27.666 0.00 0.00 *
>>
>>
>> But my job is failing, as shown below:
>>
>>
>> *[ganguly at localhost anik]$ pdb2gmx -f dna-A.pdb -o dna-B.pdb -p topol.top
>> :-) G R O M A C S (-:
>>
>> GROtesk MACabre and Sinister
>>
>> :-) VERSION 4.5.5 (-:
>>
>> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
>> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>>
>> ...................................................................................
>> ...................................................................................
>> ...................................................................................
>>
>> Opening force field file
>> /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn
>> Opening force field file
>> /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn
>> Checking for duplicate atoms....
>> Now there are 657 atoms. Deleted 7 duplicates.
>>
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 4.5.5
>> Source code file: pgutil.c, line: 91
>>
>> Fatal error:
>> Atom N3 is used in an interaction of type atom in the topology
>> database, but an atom of that name was not found in residue
>> number 31
>
> pdb2gmx can only match atom and residue names it finds in the topology
> database (.rtp). Your input structure lacks a (correctly named) N3
> atom in residue 31, which I think pdb2gmx looked for when building
> hydrogen atoms.
>
> Mark
>
>
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