Current time: 05-22-2019, 05:25 AM Hello There, Guest! (LoginRegister)


Post Reply 
 
Thread Rating:
  • 0 Votes - 0 Average
  • 1
  • 2
  • 3
  • 4
  • 5
Errors in Preparing Files for pDMD simulation
05-03-2013, 10:29 AM
Post: #1
Errors in Preparing Files for pDMD simulation
Hi,

I'm trying to use complex.linux to prepare a pdb file I have for a dmd simulation. I run into the following errors:

Quote:Complex size: 1
0:PROTEIN
5 3
Double-check the reaction range!
5 3
Double-check the reaction range!
5 2.4
Double-check the reaction range!
5 3
Double-check the reaction range!
5 3
Double-check the reaction range!
6.5 2.99
Double-check the reaction range!
2.5 2.5
Double-check the reaction range!
2.5 2.5
Double-check the reaction range!
warning: No match of atom
warning: possible error in atom name: HNE2@HIS
warning: No match of atom
warning: possible error in atom name: HD1@ASP
warning: No match of atom
warning: possible error in atom name: HD2@ASP
warning: No match of atom
warning: possible error in atom name: HE1@GLU
warning: No match of atom
warning: possible error in atom name: HE2@GLU

It still generates a state file however when I try running the simulation I get the following error message:
Quote:# Simulation box appears to be too small: 1041 atom(s) coordinates have been wrapped.
! Event list error: 1.
base: 7335 tail: 7333 nfree: 7696 nmax: 15392 nget: 68907 nrel: 61209 nget-nrel: 7698
This is a pdb file that has no ligands, just amino acids. I've tried running complex.linux with and without hydrogens. It's a fairly small simulation with only 962 atoms. Any help on this would be very much appreciated.

Thank you,

Emzo

-------------------------------
Emmanuel Lorenzo de los Santos
Mayo and Murray Groups
PhD Candidate, Bioengineering Option
California Institute of Technology
626-395-6407
Find all posts by this user
Quote this message in a reply
05-03-2013, 10:41 AM
Post: #2
RE: Errors in Preparing Files for pDMD simulation
Hi Emzo,

The messages from complex.linux are just warnings, they only mean that these hydrogen atoms explicitly listed in pdb file will not be transferred to dmd input files.

The message "Simulation box appears to be too small: " means that these atoms are outside of the simulation box, and coordinate wrapping due to periodic boundaries may cause simulation artefacts. Try to adjust box size and/or protein position so it fits into the box and see if your simulation runs after that.
Find all posts by this user
Quote this message in a reply
05-03-2013, 11:07 AM
Post: #3
RE: Errors in Preparing Files for pDMD simulation
Is there a way for me to visualize the box so I can see what the actual which atoms are out of the box and how big it should be? I tried 500 and 1000 and still got the same error.

(05-03-2013 10:41 AM)shir Wrote:  Hi Emzo,

The messages from complex.linux are just warnings, they only mean that these hydrogen atoms explicitly listed in pdb file will not be transferred to dmd input files.

The message "Simulation box appears to be too small: " means that these atoms are outside of the simulation box, and coordinate wrapping due to periodic boundaries may cause simulation artefacts. Try to adjust box size and/or protein position so it fits into the box and see if your simulation runs after that.
Find all posts by this user
Quote this message in a reply
05-03-2013, 11:50 AM
Post: #4
RE: Errors in Preparing Files for pDMD simulation
Most likely you have atoms with negative coordinates. Here is a short awk script to detect out-of-box atoms:
awk '(NR==2) {x=$1;y=$2;z=$3} (NR>3){ if ($3<0||$3>x||$4<0||$4>y||$5<0||$5>z) print "Line", NR; }' state_file

(05-03-2013 11:07 AM)emzodls Wrote:  Is there a way for me to visualize the box so I can see what the actual which atoms are out of the box and how big it should be? I tried 500 and 1000 and still got the same error.

(05-03-2013 10:41 AM)shir Wrote:  Hi Emzo,

The messages from complex.linux are just warnings, they only mean that these hydrogen atoms explicitly listed in pdb file will not be transferred to dmd input files.

The message "Simulation box appears to be too small: " means that these atoms are outside of the simulation box, and coordinate wrapping due to periodic boundaries may cause simulation artefacts. Try to adjust box size and/or protein position so it fits into the box and see if your simulation runs after that.
Find all posts by this user
Quote this message in a reply
05-03-2013, 01:15 PM
Post: #5
RE: Errors in Preparing Files for pDMD simulation
Not getting the simulation box is too small error anymore. I had the "-n" flag on because I misunderstood what it did. However, my simulation still is not running. getting this error:
Quote:! Event list error: 1.
base: 7350 tail: 7345 nfree: 7696 nmax: 15392 nget: 68922 nrel: 61221 nget-nrel: 7701

Is it maybe because of the check reaction range notifications?
Find all posts by this user
Quote this message in a reply
05-03-2013, 02:24 PM
Post: #6
RE: Errors in Preparing Files for pDMD simulation
Do you have any constraints? Could you copy here the command lines you used to generate the input files and to run dmd? Also, please, copy the simulation parameters that you supply with -i option.

(05-03-2013 01:15 PM)emzodls Wrote:  Not getting the simulation box is too small error anymore. I had the "-n" flag on because I misunderstood what it did. However, my simulation still is not running. getting this error:
Quote:! Event list error: 1.
base: 7350 tail: 7345 nfree: 7696 nmax: 15392 nget: 68922 nrel: 61221 nget-nrel: 7701

Is it maybe because of the check reaction range notifications?
Find all posts by this user
Quote this message in a reply
Post Reply 


Forum Jump:


User(s) browsing this thread: 1 Guest(s)