On 4/4/13 6:17 PM, Juliette N. wrote:
Hi Justin,
Thanks a lot for your message. I am petrified why pdb2gmx is not
recognizing the residue ETY. This the first residue added to ffoplsaa.rtp
but as you may see below it is not read from rtp.
I am sure this residue is added to ffoplsaa.rtp which is existing in the
working directory:
[ ETY ]
[ atoms ]
C1 opls_143 -0.120 1
H11 opls_144 0.060 1
H12 opls_144 0.060 1
C2 opls_143 -0.120 2
H21 opls_144 0.060 2
H22 opls_144 0.060 2
[ bonds ]
C1 H11
C1 H12
C1 C2
C2 H21
C2 H22
;C2 C1
Then I issue:
pdb2gmx -f Ethylene.gro -o GRO.gro -p Ethylene.top -ff oplsaa
:-) G R O M A C S (-:
GROwing Monsters And Cloning Shrimps
:-) VERSION 4.5.4 (-:
Using the Oplsaa force field in directory oplsaa.ff
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermodels.dat
Select the Water Model:
1: TIP4P TIP 4-point, recommended
2: TIP3P TIP 3-point
3: TIP5P TIP 5-point
4: SPC simple point charge
5: SPC/E extended simple point charge
6: None
6
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading Ethylene.gro...
Read 'Giant Rising Ordinary Mutants for A Clerical Setup', 6 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 1 residues with 6 atoms
chain #res #atoms
1 ' ' 1 6
No occupancies in Ethylene.gro
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 56
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
Back Off! I just backed up Ethylene.top to ./#Ethylene.top.1#
Processing chain 1 (6 atoms, 1 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue ETY1 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 4.5.4
Source code file: resall.c, line: 581
Fatal error:
Residue 'ETY' 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
I am kind of baffled what could be wrong. I would really appreciate if you
could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I
doubt)?
Do i have to edit esiduetypes.dat?
You've added the .rtp entry incorrectly. pdb2gmx in version 4.5 and above needs
.rtp files to be organized in force field subdirectories (in your case
oplsaa.ff). It will not recognize a file called "ffoplsaa.rtp," which is the
pre-4.5 syntax for force field files.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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
