shahid nayeem wrote:
Dear All
I used the following command sequentially to prepare file for energy
minimization and subsequent MD run.
1. pdb2gmx -f *.pdb -o seq.gro -p seq.top
2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp
grompp gives following error.processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 279 of the 1225 non-bonded parameter combinations
ERROR 1 [file seq.top, line 1965]:
No default G96Bond types
ERROR 2 [file seq.top, line 5271]:
No default G96Angle types
ERROR 3 [file seq.top, line 5272]:
No default G96Angle types
ERROR 4 [file seq.top, line 5648]:
No default G96Angle types
ERROR 5 [file seq.top, line 5653]:
No default G96Angle types
ERROR 6 [file seq.top, line 5654]:
No default G96Angle types
ERROR 7 [file seq.top, line 5655]:
No default G96Angle types
ERROR 8 [file seq.top, line 5656]:
No default G96Angle types
ERROR 9 [file seq.top, line 6201]:
No default Proper Dih. types
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file seq.top, line 6932]:
System has non-zero total charge: 7.000001e+00
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
There was 1 note
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: grompp.c, line: 986
Fatal error:
There were 9 errors in input file(s)
-------------------------------------------------------
pdb2gmx works properly using ff43a1 forcefield. My protein contains
Heme. I was having N-terminal ACE group which I simply deleted from
the pdb.
Am I right in deleting this group. How should I proceed to get rid of
this error.
That seems like a particularly poor solution. Simply getting rid of an
inconvenient group does not sound appropriate. Ask yourself whether or not
there is some functionally significant reason to having the ACE group there
(chain truncation? artificial modification?) and decide.
As for the errors, look into the topology to see which atoms are causing the
problems. Then decide if there are indeed appropriate parameters in the force
field for this task.
-Justin
Thanks in anticipation of help.
Shahid Nayeem
--
========================================
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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