[gmx-users] ionomer topolgy
Ehsan Sadeghi
esa38 at sfu.ca
Sat Sep 28 02:43:02 CEST 2013
Thanks for your prompt response. I made the modifications on the aminoacids.rtp file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff.
I did not modify any force field. I thought I still can use the default force field in gromos; isn't it right?
Here is the output from pdb2gmx. Thank you for your consideration.
-----------------------------------
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading nafion3.pdb...
WARNING: all CONECT records are ignored
Read 46 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 0 residues with 46 atoms
chain #res #atoms
1 'G' 1 24
2 'H' 1 22
WARNING: there were 1 atoms with zero occupancy and 45 atoms with
occupancy unequal to one (out of 46 atoms). Check your pdb file.
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp
Atomtype 1
Reading residue database... (gromos53a6)
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper dihedral
Residue 108
Sorting it all out...
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.36#
Processing chain 1 'G' (24 atoms, 1 residues)
Warning: Starting residue LI0 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.3
Source code file: /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642
Fatal error:
Residue 'LI' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Thanks,
Ehsan
----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Friday, September 27, 2013 3:06:05 PM
Subject: Re: [gmx-users] ionomer topolgy
On 9/27/13 5:53 PM, Ehsan Sadeghi wrote:
> Hello,
>
> I revised my pdb and rtp files. I still receive similar error message.
>
Whatever modifications you're making probably aren't being done in the right
files. You haven't yet responded to my question about which force field you're
using and whether you're making modifications in the working directory or in
$GMXLIB. Exact screen output from pdb2gmx would be very useful here. Please
post the exact command and all screen output, including your selections and the
error message.
-Justin
> Here are the new files:
>
> .pdb:
>
> ATOM 1 C1 LIG 1 -10.450 5.214 -1.717 1.00 0.00 C
> ATOM 2 C2 LIG 1 -8.424 5.477 -1.030 1.00 0.00 C
> ATOM 3 C3 LIG 1 -6.603 5.864 -0.166 1.00 0.00 C
> ATOM 4 F1 LIG 1 -6.651 6.230 -1.691 1.00 0.00 F
> ATOM 5 F2 LIG 1 -8.417 4.546 -2.349 1.00 0.00 F
> ATOM 6 C4 LIG 1 -5.705 3.003 1.204 1.00 0.00 C
> ATOM 7 F3 LIG 1 -7.247 5.032 1.683 1.00 0.00 F
> ATOM 8 F4 LIG 1 -8.521 5.307 0.400 1.00 0.00 F
> ATOM 9 C5 LIG 1 -3.913 4.878 2.109 1.00 0.00 C
> ATOM 10 F5 LIG 1 -4.358 3.650 -0.024 1.00 0.00 F
> ATOM 11 F6 LIG 1 -6.198 1.346 0.214 1.00 0.00 F
> ATOM 12 C6 LIG 1 -1.306 5.673 2.286 1.00 0.00 C
> ATOM 13 F7 LIG 1 -3.429 3.111 0.668 1.00 0.00 F
> ATOM 14 F8 LIG 1 -2.358 3.855 1.570 1.00 0.00 F
> ATOM 15 C7 LIG 1 0.246 3.040 2.048 1.00 0.00 C
> ATOM 16 F9 LIG 1 -0.514 4.358 3.241 1.00 0.00 F
> ATOM 17 F10 LIG 1 -0.928 3.807 1.741 1.00 0.00 F
> ATOM 18 C8 LIG 1 1.925 3.706 2.014 1.00 0.00 C
> ATOM 19 F11 LIG 1 -0.226 2.548 0.094 1.00 0.00 F
> ATOM 20 F12 LIG 1 0.215 1.482 1.590 1.00 0.00 F
> ATOM 21 F13 LIG 1 -11.789 4.355 -2.598 1.00 0.00 F
> ATOM 22 F14 LIG 1 -11.552 4.133 -0.632 1.00 0.00 F
> ATOM 23 F15 LIG 1 2.299 2.385 2.438 1.00 0.00 F
> ATOM 24 F16 LIG 1 1.831 1.994 1.526 1.00 0.00 F
> ATOM 25 O1 SCH 2 3.334 3.720 1.360 1.00 0.00 O
> ATOM 26 C1 SCH 2 5.273 2.985 0.897 1.00 0.00 C
> ATOM 27 C2 SCH 2 6.100 2.445 1.642 1.00 0.00 C
> ATOM 28 F1 SCH 2 4.528 2.997 1.631 1.00 0.00 F
> ATOM 29 F2 SCH 2 6.122 3.473 0.467 1.00 0.00 F
> ATOM 30 C3 SCH 2 7.274 1.746 2.026 1.00 0.00 C
> ATOM 31 O2 SCH 2 5.454 2.160 2.446 1.00 0.00 O
> ATOM 32 F3 SCH 2 6.788 2.944 0.993 1.00 0.00 F
> ATOM 33 F4 SCH 2 7.031 1.025 2.779 1.00 0.00 F
> ATOM 34 F5 SCH 2 8.010 2.431 2.393 1.00 0.00 F
> ATOM 35 F6 SCH 2 7.678 1.241 1.173 1.00 0.00 F
> ATOM 36 C4 SCH 2 5.042 1.305 2.243 1.00 0.00 C
> ATOM 37 C5 SCH 2 5.168 0.043 2.583 1.00 0.00 C
> ATOM 38 F7 SCH 2 4.938 1.296 1.178 1.00 0.00 F
> ATOM 39 F8 SCH 2 4.377 1.446 3.070 1.00 0.00 F
> ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S
> ATOM 41 F9 SCH 2 4.304 0.015 3.213 1.00 0.00 F
> ATOM 42 F10 SCH 2 6.073 0.088 2.014 1.00 0.00 F
> ATOM 43 O3 SCH 2 4.555 -2.079 3.473 1.00 0.00 O
> ATOM 44 H SCH 2 4.772 -3.020 3.567 1.00 0.00 H
> ATOM 45 O4 SCH 2 6.692 -1.508 1.977 1.00 0.00 O
> ATOM 46 O5 SCH 2 6.001 -2.846 2.762 1.00 0.00 O
> ----------------------------------
> .rtp
>
> [ LIG ]
> [ atoms ]
> C1 C 0.000 0
> C2 C 0.000 0
> C3 C 0.000 0
> F1 F 0.000 0
> F2 F 0.000 0
> C4 C 0.000 0
> F3 F 0.000 0
> F4 F 0.000 0
> C5 C 0.000 0
> F5 F 0.000 0
> F6 F 0.000 0
> C6 C 0.000 0
> F7 F 0.000 0
> F8 F 0.000 0
> C7 C 0.000 0
> F9 F 0.000 0
> F10 F 0.000 0
> C8 C 0.000 0
> F11 F 0.000 0
> F12 F 0.000 0
> F13 F 0.000 0
> F14 F 0.000 0
> F15 F 0.000 0
> F16 F 0.000 0
>
> [ SCH ]
> [ atoms ]
> O1 OM 0.000 0
> C1 C 0.000 0
> C2 C 0.000 0
> F1 F 0.000 0
> F2 F 0.000 0
> C3 C 0.000 0
> O2 OM 0.000 0
> F3 F 0.000 0
> F4 F 0.000 0
> F5 F 0.000 0
> F6 F 0.000 0
> C4 C 0.000 0
> C5 C 0.000 0
> F7 F 0.000 0
> F8 F 0.000 0
> S S 0.000 0
> F9 F 0.000 0
> F10 F 0.000 0
> O3 O 0.000 0
> H H 0.000 0
> O4 O 0.000 0
> O5 O 0.000 0
>
>
> Thanks,
> Ehsan
>
> ----- Original Message -----
> From: "Justin Lemkul" <jalemkul at vt.edu>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Friday, September 27, 2013 1:24:44 PM
> Subject: Re: [gmx-users] ionomer topolgy
>
>
>
> On 9/27/13 4:18 PM, Ehsan Sadeghi wrote:
>> Hi,
>>
>> I just added this to the existing .rtp file in gromos
>>
>> [ LIG ]
>> [ atoms ]
>> C C 0.000 0
>> F F 0.000 0
>>
>> [ SCH ]
>> [ atoms ]
>> O OM 0.000 0
>> C C 0.000 0
>> O O 0.000 0
>> F F 0.000 0
>> S S 0.000 0
>> H H 0.000 0
>>
>> I also added LIG and SCH to the residuetypes.dat
>>
>
> Your definition of "LIG" in the .rtp entry does not come anywhere close to
> matching what is in the .pdb file. If, in fact, each residue only has two atoms
> (I don't see how that's chemically possible), then your residue numbers have to
> follow suit. As it stands now, pdb2gmx is trying to find a 24-atom LIG residue
> and a 22-atom SCH. Neither of these is true, per the .rtp.
>
> -Justin
>
>> Kind regards,
>> Ehsan
>>
>> ----- Original Message -----
>> From: "Justin Lemkul" <jalemkul at vt.edu>
>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Sent: Friday, September 27, 2013 12:29:38 PM
>> Subject: Re: [gmx-users] ionomer topolgy
>>
>>
>>
>> On 9/27/13 3:17 PM, Ehsan Sadeghi wrote:
>>> Many thanks Justin.
>>>
>>> Here is my .pdb file:
>>>
>>> ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C
>>> ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C
>>> ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C
>>> ATOM 4 F LIG 1 -6.651 6.230 -1.691 1.00 0.00 F
>>> ATOM 5 F LIG 1 -8.417 4.546 -2.349 1.00 0.00 F
>>> ATOM 6 C LIG 1 -5.705 3.003 1.204 1.00 0.00 C
>>> ATOM 7 F LIG 1 -7.247 5.032 1.683 1.00 0.00 F
>>> ATOM 8 F LIG 1 -8.521 5.307 0.400 1.00 0.00 F
>>> ATOM 9 C LIG 1 -3.913 4.878 2.109 1.00 0.00 C
>>> ATOM 10 F LIG 1 -4.358 3.650 -0.024 1.00 0.00 F
>>> ATOM 11 F LIG 1 -6.198 1.346 0.214 1.00 0.00 F
>>> ATOM 12 C LIG 1 -1.306 5.673 2.286 1.00 0.00 C
>>> ATOM 13 F LIG 1 -3.429 3.111 0.668 1.00 0.00 F
>>> ATOM 14 F LIG 1 -2.358 3.855 1.570 1.00 0.00 F
>>> ATOM 15 C LIG 1 0.246 3.040 2.048 1.00 0.00 C
>>> ATOM 16 F LIG 1 -0.514 4.358 3.241 1.00 0.00 F
>>> ATOM 17 F LIG 1 -0.928 3.807 1.741 1.00 0.00 F
>>> ATOM 18 C LIG 1 1.925 3.706 2.014 1.00 0.00 C
>>> ATOM 19 F LIG 1 -0.226 2.548 0.094 1.00 0.00 F
>>> ATOM 20 F LIG 1 0.215 1.482 1.590 1.00 0.00 F
>>> ATOM 21 F LIG 1 -11.789 4.355 -2.598 1.00 0.00 F
>>> ATOM 22 F LIG 1 -11.552 4.133 -0.632 1.00 0.00 F
>>> ATOM 23 F LIG 1 2.299 2.385 2.438 1.00 0.00 F
>>> ATOM 24 F LIG 1 1.831 1.994 1.526 1.00 0.00 F
>>> ATOM 25 OM SCH 2 3.334 3.720 1.360 1.00 0.00 O
>>> ATOM 26 C SCH 2 5.273 2.985 0.897 1.00 0.00 C
>>> ATOM 27 C SCH 2 6.100 2.445 1.642 1.00 0.00 C
>>> ATOM 28 F SCH 2 4.528 2.997 1.631 1.00 0.00 F
>>> ATOM 29 F SCH 2 6.122 3.473 0.467 1.00 0.00 F
>>> ATOM 30 C SCH 2 7.274 1.746 2.026 1.00 0.00 C
>>> ATOM 31 OM SCH 2 5.454 2.160 2.446 1.00 0.00 O
>>> ATOM 32 F SCH 2 6.788 2.944 0.993 1.00 0.00 F
>>> ATOM 33 F SCH 2 7.031 1.025 2.779 1.00 0.00 F
>>> ATOM 34 F SCH 2 8.010 2.431 2.393 1.00 0.00 F
>>> ATOM 35 F SCH 2 7.678 1.241 1.173 1.00 0.00 F
>>> ATOM 36 C SCH 2 5.042 1.305 2.243 1.00 0.00 C
>>> ATOM 37 C SCH 2 5.168 0.043 2.583 1.00 0.00 C
>>> ATOM 38 F SCH 2 4.938 1.296 1.178 1.00 0.00 F
>>> ATOM 39 F SCH 2 4.377 1.446 3.070 1.00 0.00 F
>>> ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S
>>> ATOM 41 F SCH 2 4.304 0.015 3.213 1.00 0.00 F
>>> ATOM 42 F SCH 2 6.073 0.088 2.014 1.00 0.00 F
>>> ATOM 43 O SCH 2 4.555 -2.079 3.473 1.00 0.00 O
>>> ATOM 44 H SCH 2 4.772 -3.020 3.567 1.00 0.00 H
>>> ATOM 45 O SCH 2 6.692 -1.508 1.977 1.00 0.00 O
>>> ATOM 46 O SCH 2 6.001 -2.846 2.762 1.00 0.00 O
>>> CONECT 1 2 21 22
>>> CONECT 2 1 3 4 5
>>> CONECT 2
>>> CONECT 3 2 6 7 8
>>> CONECT 3
>>> CONECT 4 2
>>> CONECT 5 2
>>> CONECT 6 3 9 10 11
>>> CONECT 6
>>> CONECT 7 3
>>> CONECT 8 3
>>> CONECT 9 6 12 13 14
>>> CONECT 9
>>> CONECT 10 6
>>> CONECT 11 6
>>> CONECT 12 9 15 16 17
>>> CONECT 12
>>> CONECT 13 9
>>> CONECT 14 9
>>> CONECT 15 12 18 19 20
>>> CONECT 15
>>> CONECT 16 12
>>> CONECT 17 12
>>> CONECT 18 15 23 24 25
>>> CONECT 18
>>> CONECT 19 15
>>> CONECT 20 15
>>> CONECT 21 1
>>> CONECT 22 1
>>> CONECT 23 18
>>> CONECT 24 18
>>> CONECT 25 18 26
>>> CONECT 26 25 27 28 29
>>> CONECT 26
>>> CONECT 27 26 30 31 32
>>> CONECT 27
>>> CONECT 28 26
>>> CONECT 29 26
>>> CONECT 30 27 33 34 35
>>> CONECT 30
>>> CONECT 31 27 36
>>> CONECT 32 27
>>> CONECT 33 30
>>> CONECT 34 30
>>> CONECT 35 30
>>> CONECT 36 31 37 38 39
>>> CONECT 36
>>> CONECT 37 36 40 41 42
>>> CONECT 37
>>> CONECT 38 36
>>> CONECT 39 36
>>> CONECT 40 37 43 45 46
>>> CONECT 40
>>> CONECT 41 37
>>> CONECT 42 37
>>> CONECT 43 40 44
>>> CONECT 44 43
>>> CONECT 45 40
>>> CONECT 46 40
>>> MASTER 0 0 0 0 0 0 0 0 46 0 46 0
>>> END
>>>
>>> -------------------------------------------------
>>> I already added LIG and SCH in residuetypes.dat and defined the atoms for each residue in aminoacids.rtp in gromos. When I run pdb2gmx -f nafion.pdb
>>> I receive this error:
>>>
>>>
>>> Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA.
>>> Warning: Starting residue SCH2 in chain not identified as Protein/RNA/DNA.
>>> Problem with chain definition, or missing terminal residues.
>>> This chain does not appear to contain a recognized chain molecule.
>>> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
>>> 8 out of 8 lines of specbond.dat converted successfully
>>>
>>> -------------------------------------------------------
>>> Program pdb2gmx, VERSION 4.6.3
>>> Source code file: /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642
>>>
>>> Fatal error:
>>> Residue 'LIG' not found in residue topology database
>>> For more information and tips for troubleshooting, please check the GROMACS
>>>
>>
>> You still haven't provided any real useful diagnostic information. What do the
>> .rtp entries look like? Which force field did you modify? Did you modify a
>> local copy of it, or the one in $GMXLIB? Based on that, are you making the
>> right choice when running pdb2gmx?
>>
>> -Justin
>>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
==================================================
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