shahid nayeem wrote:
HI
I am using Cytochrome-C pdb 1hrc.pdb. In pdb2gmx it does not gives
any eror using ffG43a1. .top file produced shows all bonds (Fe & SD of
MET 80 and Fe & NE2 of HIS 18) using spec.dat file but all the error
lines does not have bond/angle nomenclature such as
809 810 2 gb_30
810 811 2 gb_29
810 1068 2
812 813 2 gb_4
812 814 2 gb_9
814 815 2 gb_2
810 atom SD of MET80 and 1068 is Fe of Heme. I tried modifying .rtp
file of force-field and adding these bonds and giving some name to it
but got the same error in grompp.
Modifying an .rtp entry will do nothing since this bond exists between two
(presumably) non-sequential residues.
Though .top file shows these bonds the .gro file generated does not
show these bonds in VMD while original pdb file shows these bonds.
thanking you.
VMD's concept of bonds is irrelevant, it's simply guessing where they should be
based on interatomic distances.
Unfortunately, GROMACS does not work "out of the box" with heme-containing
species, but these types of simulations are in no way novel, so obviously
parameters for these missing terms should be available somewhere. Consult the
literature, and if necessary, contact the authors of relevant papers - they
should be able to reproduce their work, at least, we hope :)
-Justin
waiting for your suggestion.
shahid Nayeem
On 7/15/10, Justin A. Lemkul <[email protected]> wrote:
shahid nayeem wrote:
Hi Justin
These errors are from bond between MET/HIS residue and Heme group of
my protein. I checked for all these nine errors of bond and angle in
th file ffG43a1bon.itp and I couldnt find these defined in this file.
Using other options of force field also gives error at some point.
waiting for your suggestion to proceed further.
One of the most important choices when conducting MD simulations is the
force
field. You'll have to find one that works. It appears that (unfortunately)
the
Gromos force fields do not work out of the box when heme is involved.
If you want specific advice about other force fields, you'll have to
describe
your problem much better than "gives error at some point." No one can help
you
sort that out. You'd do well to look into the literature. Simulations of
heme
proteins are not novel, so clearly others have made this work, and in some
cases, parameters might be provided for the terms that are missing.
-Justin
shahid Nayeem
On 7/15/10, Justin A. Lemkul <[email protected]> wrote:
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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--
========================================
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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