tekle...@ualberta.ca wrote:
Hi Justine,
Here is the procedure I followed….
I developed my PDB structure (non-protein means it is a polymer called
PAP) using Material studio…. Get the PDB file and process it using the
PRODRG…. I got both the GRO and TOP files………. However, PRODRG gave me a
TOP and GRO file for a deprotonation carboxylic acid functional group,
so I have to modify it my self as follows.
Manual hacking should not be necessary. See the PRODRG FAQ regarding the
ADDHYD/DELHYD commands.
Inside the initial Topology
44 CH1 1 UNK CA 13 0.143 13.0190
45 C 1 UNK C 13 0.372 12.0110
46 OM 1 UNK OXT 13 -0.757 15.9994
47 OM 1 UNK O 13 -0.758 15.9994
The modified topology
Which means I have manually modified the entire topology by including
the H group (HO) in the COO- functional group....
=============================================
44 CH1 1 PAP CA 13 0.000 13.0190
45 C 1 PAP C 13 0.530 12.0110
46 O 1 PAP OXT 13 -0.380 15.9994
47 OA 1 PAP O 13 -0.548 15.9994
48 HO 1 PAP HAA 13 0.398 1.00800
==============================================
So from 54 atoms now became 55 atoms and their order is also rearranged
…. To match the GRO file. I took the charges from the asparagines
residue for the carboxylic acid in the ffgmx.
I assume you mean protonated aspartate, and that seems reasonable enough to do.
I have modified the GRO file as well because the coordinated are for 54
but now I have included the H atom at the right position…… I visualized
that and it worked fine….
Hence this is a new amino acid residue now as it does not exist in the
residue database….
I have chosen the ffgmx force field since the other force fields does
not allow me to go through… therefore I included this force field using
Well, there has to be a reason. You can develop parameters for any force field.
I'm not saying ffgmx is the root cause of your problem, but choosing a force
field simply because it seemed to be the most convenient is a really lousy way
to make an extremely important choice.
; Include forcefield parameters
#include "ffgmx.itp"
[ moleculetype ]
; Name nrexcl
PAP 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 PAP CAZ 1 0.000 15.0350
2 CH2 1 PAP CAK 1 0.000 14.0270
-
-
-
; Include Toluene topology
#include "Toluene.itp"
#ifdef posres
Watch your capitalization - see the note below.
; Position restraint for PAP
[ position_restraints ]
#include "posres.itp"
#endif
[ System ]
; Name
PAP in Toluene
[ molecules ]
; Compound #mols
PAP 1
Energy minimization
grompp -v -f minim.mdp -c PAP.gro -p PAP.top -PAPX.tpr
mdrun –v deffnm PAP.tpr
Now the Construction of the Box….multiple conformations … in this case 8
molecules
genconf –f PAPX.grob –nbox 2 2 2 –rot –dist 0.1 0.1 0.1 –o PAPY.gro
Followed by………………….
But I want to enlarge the whole box ………………
Editconf –f PAPY.gro –box 10 10 10 PAPZ.gro
I checked the GRO file and the volume changed from 4.3 4.3 4.3 to 10 by
10 by 10
Energy minimization…………of the SYSTEM followed by SOLVATION with toluene..
genbox –cp PAPZ.gro –cs toluene.gro –o PAPD.gro
<snip>
Energy minimization of the system …. I just also check the distance of
each solvent molecule and they are not overlapped each other as the
–dist option is set a little big…
It converged to Potential Energy 1.362e+05
Max force = 5.3+1
Norm of force = 1.287
For Fmax less than 100………………………It converged in 11351!
I don't understand what you mean here. Your Fmax appears to be 53, not 11351.
If it is actually 11351, then there is a huge repulsive force somewhere in the
system (mdrun prints the atom number). Furthermore, your potential energy is a
very large, positive number, indicating repulsive interactions in your system.
This is probably the root cause of your problems. There are some bad steric
clashes somewhere, or the parameters for some species (either PAP or TOL) are
unreasonable.
I checked the volume is 1000 and density is 644 and total mol is 3435……
Now I want to relax my system…………..
Position restrain……………….. using.............. It run for long and all of
a sudden it crushed ….
The following error…………………………………………
For readability, please use some semblance of normal punctuation :)
<snip>
OK, so your system is blowing up. See the page of the same title on the Gromacs
site for general tips, but it probably stems from the ridiculously high
(repulsive) potential, and perhaps the huge Fmax (which is unclear above).
Your .mdp files look reasonable enough, except that -DFLEXBILE int the em.mdp
file really isn't doing anything if you don't have water in your system. Of
potential note - in your topology, you have an "#ifdef posres" statement, but
then you use "-DPOSRES" in the pr.mdp file; I do not know if such things are
case-sensitive, but I suspect they are.
I need your HELP!!!!!!!!!!!!!!!!!!!! I spent lots of time trying to
figure out this!!!!
No need to shout :) It's very hard to figure out someone else's problem via
email, especially over the course of several days and while in the midst of
one's own work.
-Justin
Rob
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
tekle...@ualberta.ca wrote:
Hi Justin,
I just checked this error on the archive list but could not found a
reasonable answer ......
I have done the energy minimization and it is ok Fmax less than 100
but when I start equilibrating my system I got the following error..
=================================================
There were 2 inconsistent shifts. Check your topology
Warning: 1-4 interaction between 18851 and 18856 at distance 42.558
which is larger than the 1-4 table size 1.900 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
Here's the usual advice:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
<snip>
tcoupl = V-rescale ; modified berendsen thermostat
; Groups to couple separately
tc-grps = PAP TOL
What are PAP and TOL? Are they of sufficient size to justify their
own temperature coupling groups?
http://www.gromacs.org/Documentation/Terminology/Thermostats
Other than that, you'll have to give some information about what your
system is, how you built it, and what parameters (force field) you're
using.
-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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