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" <jalem...@vt.edu>
To: "Discussion list for GROMACS users" <gmx-users@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" <jalem...@vt.edu>
To: "Discussion list for GROMACS users" <gmx-users@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
