Hsin-Lin Chiang wrote:
Hi everyone,
My pdb file is consist of two chains with one intra- two
inter-disulfide bonds.
So I used pdb2gmx in this way
pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep ter
(I have deleted the TER and OXT lines of A-chain.)
I'm not sure if I need to use -ter here, I don't understand the meaning
of "interective termini selection, iso charged ."
The -ter option allows you to change the protonation state of the termini. The
shorthand "iso" means "instead of," implying that charged termini are the
default. If you do not need to alter the protonation state of the termini, then
you do not need the -ter option.
Anyway, I met problem after editconf, genbox, grompp, genion, and grompp.
When I execute mdrun,
I got the warning and terminated.
Please see the long message below my name.
Your system exploded because pdb2gmx likely tried to make your two chains one
continuous protein, forming an unrealistic bond between the C-terminal of chain
A and the N-terminal of chain B. By removing the TER delimiter, you've
essentially told pdb2gmx that you have one protein, not two.
However, if I used pdb2gmx in this way
pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep
interactive
and selected y.
Then everything is OK in mdrun step.
I don't know what the different in -chainsep interactive and -chainsep
ter is in my case.
Assuming that the "y" response indicates that you want separate chains, that's
why this approach works. Regardless, if you have two distinct proteins (i.e.
the backbones are not continuous), you do not want the chains to be considered
continuous. Disulfides are created in a separate mechanism utilizing
specbond.dat and is independent of the use of -chainsep.
They seems to the same in my two chain system.
There is likely some difference (probably a single bond) that is causing the
problem.
-Justin
Sincerely yours,
Hsin-Lin
-------------------------------------------------
starting mdrun 'Protein in water'
7500000 steps, 15000.0 ps.
Warning: 1-4 interaction between 196 and 207 at distance 3.231 which is
larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 66.078426, max 708.612183 (between atoms 207 and 208)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
207 208 90.0 0.1000 70.9612 0.1000
Back Off! I just backed up step0b.pdb to ./#step0b.pdb.4#
Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4#
Wrote pdb files with previous and current coordinates
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 67071649.681650, max 719263296.000000 (between atoms 207 and 208)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
207 208 90.0 70.9612 71926328.0000 0.1000
212 213 90.0 0.1090 0.1308 0.1090
216 217 40.3 0.1090 0.1090 0.1090
218 219 90.0 0.1090 0.1545 0.1090
224 225 90.0 0.1000 0.3996 0.1000
232 233 90.0 0.1000 0.3867 0.1000
238 239 90.0 0.1000 0.1782 0.1000
238 240 90.0 0.1000 1.0652 0.1000
243 244 90.0 0.1000 0.3092 0.1000
250 251 90.0 0.1000 0.3082 0.1000
250 252 90.0 0.1000 0.2102 0.1000
step 1: Water molecule starting at atom 10744 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Back Off! I just backed up step1b.pdb to ./#step1b.pdb.4#
Back Off! I just backed up step1c.pdb to ./#step1c.pdb.4#
Wrote pdb files with previous and current coordinates
Segmentation fault
--
========================================
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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