francesca vitalini wrote:
Do you mean that I can just use the new version of pdb2gmx than change
the included forcefield and in case the name of the atoms and it
should work?
You still have to fix the incorrect atom name(s), regardless of version. You
can use a new version to make use of pdb2gmx -ter, if necessary. Otherwise,
your version should work for what you need.
-Justin
2012/2/16 Justin A. Lemkul <jalem...@vt.edu>:
francesca vitalini wrote:
Hi all!
I'm trying to create a topology file from the pdb using the pdb2gmx
command of gromacs 3.3.1 but I'm encountering some issues. I should
use the flag -tar in order to select interactively the termini, but
with the old version of gromacs this is not implemented and I cannot
use a new one because I need the reverse transformation tool which is
only implemented in that version.
The topology format is largely unaffected by differences in version. A few
moments with a text editor to fix the #include statements written by a
version in the 4.5.x series would solve any problems.
Here it is the pdb I'm using
REMARK
ATOM 1 1HH3 ACE 1 -3.547 1.520 1.054
ATOM 2 CH3 ACE 1 -3.081 0.536 0.999
ATOM 3 2HH3 ACE 1 -3.437 0.016 0.110
ATOM 4 3HH3 ACE 1 -3.348 -0.041 1.883
ATOM 5 C ACE 1 -1.570 0.683 0.929
ATOM 6 O ACE 1 -1.051 1.800 0.938
ATOM 7 N ALA 2 -0.862 -0.446 0.851
ATOM 8 H ALA 2 -1.368 -1.322 0.859
ATOM 9 CA ALA 2 0.607 -0.509 0.828
ATOM 10 HA ALA 2 0.997 0.272 1.484
ATOM 11 CB ALA 2 1.025 -1.867 1.412
ATOM 12 1HB ALA 2 2.113 -1.918 1.485
ATOM 13 2HB ALA 2 0.676 -2.677 0.770
ATOM 14 3HB ALA 2 0.604 -1.990 2.411
ATOM 15 C ALA 2 1.238 -0.262 -0.565
ATOM 16 O ALA 2 2.465 -0.181 -0.678
ATOM 17 N NAC 3 0.423 -0.139 -1.620
ATOM 18 H NAC 3 -0.569 -0.212 -1.447
ATOM 19 CH3 NAC 3 0.860 0.098 -2.992
ATOM 20 1HH3 NAC 3 1.413 1.037 -3.050
ATOM 21 2HH3 NAC 3 1.506 -0.718 -3.323
ATOM 22 3HH3 NAC 3 -0.006 0.155 -3.652
TER
END
And this is the pdb2gmx command
path/pdb2gmx -ignh -missing -f struct1-1.pdb -p ala.top -o ala.gro
I use the gromos9653a6 forcefield and the spc water model
And this is the error I get
There are 2 donors and 2 acceptors
There are 2 hydrogen bonds
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2gmx.c, line: 383
Fatal error:
Atom CH3 in residue ACE 1 not found in rtp entry with 3 atoms
while sorting atoms
-------------------------------------------------------
Any suggestions?
Check the .rtp file - your atom is named in a way that is inconsistent with
what the force field expects.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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