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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