Why do I get this error while running psfgen for NAMD?

Urszula Sylwia Uciechowska-Kaczmarzyk @Urszula_Uciechowska-Kaczmarzyk

01 January 2015 9 416 Report

I want to run dsDNA-protein MD simulations.

I have tried to use top_all36_na.rtf I

prepared a script to run psfgen:

package require psfgen

resetpsf

topology charmm36.nbfix/top_all36_na.rtf

topology charmm36.nbfix/top_all36_prot.rtf

topology charmm36.nbfix/top_water_ions.rtf

mol new prot-DNA.pdb

set sel [atomselect top protein]

set chains [lsort -unique [$sel get chain]] ;# return A

foreach chain $chains {

puts "Adding protein chain $chain to psfgen"

set seg ${chain}PRO

set sel [atomselect top "protein and chain $chain"]

$sel set segid $seg

$sel writepdb tmp.pdb

segment $seg { pdb tmp.pdb }

coordpdb tmp.pdb

}

set sel [atomselect top nucleic]

set chains [lsort -unique [$sel get chain]] ;# return A B C D

foreach chain $chains {

puts "Adding DNA chain $chain to psfgen"

set seg ${chain}DNA

set sel [atomselect top "nucleic and chain $chain"]

$sel set segid $seg

$sel writepdb tmp.pdb

segment $seg { pdb tmp.pdb }

set resids [lsort -unique [$sel get resid]]

foreach r $resids {

patch DEOX $seg:$r

}

regenerate angles dihedrals

coordpdb tmp.pdb

}

guesscoord

after that I am getting:

Adding DNA chain B to psfgen

psfgen) building segment BDNA

psfgen) reading residues from pdb file tmp.pdb

psfgen) extracted 46 residues from pdb file

psfgen) Info: generating structure...psfgen) Info: skipping conformation

O3'-O5'-P-O2P at beginning of segment.

psfgen) Info: skipping conformation O3'-O5'-P-O1P at beginning of segment.

psfgen) Info: skipping conformation O3'-P-O5'-C5' at beginning of segment.

psfgen) Info: skipping bond O3'-P at end of segment.

psfgen) Info: skipping conformation C3'-O3'-P-O5' at end of segment.

psfgen) Info: skipping conformation C4'-C3'-O3'-P at end of segment.

segment complete.

psfgen) applying patch DEOX to 1 residues

psfgen) regenerating all angles

psfgen) regenerating all dihedrals

psfgen) reading coordinates from pdb file tmp.pdb

psfgen) Warning: failed to set coordinate for atom C7 THY:288 BDNA

psfgen) Warning: failed to set coordinate for atom C7 THY:291 BDNA

psfgen) Warning: failed to set coordinate for atom C7 THY:292 BDNA

psfgen) Warning: failed to set coordinate for atom C7 THY:298 BDNA

psfgen) Warning: failed to set coordinate for atom C7 THY:299 BDNA

psfgen) Warning: failed to set coordinate for atom C7 THY:310 BDNA

psfgen) Warning: failed to set coordinate for atom C7 THY:316 BDNA

psfgen) Warning: failed to set coordinate for atom C7 THY:321 BDNA

psfgen) Warning: failed to set coordinate for atom C7 THY:323 BDNA

psfgen) Warning: failed to set coordinate for atom C7 THY:330 BDNA

What did go wrong?

Could someone please let me know what sort of mistake I've probably made

here?

Paolo Piazzetta

First of all I want to point out that I always worked with protein and enzymes. However your problem seems to be linked to C7 atom of THY that does not find correspondence in the topology file. As matter of fact I checked in the top_all36_na.rtf and there is no description of the C7 in the RESI THY. Before to run the psf building script you have to be sure that your system is fully described in the top file you are using.

Paolo

Urszula Sylwia Uciechowska-Kaczmarzyk

Thank you for your reply, I am new to NAMD. I took this top_all36_na.rtf as it was also used in NAMD tutorial regarding MD simulation of DNA-prtoein, which file should I use then? Where can I find other rtf files? how should I check which one will be suitable for my system.

Dear Urszula, in this case is necessary to learn how to manage with the psf building procedure gradually. I suppose that the comprehension of the script you are using is limited. The NAMD tutorial that you cited involves a standard DNA-protein model which is probably slightly different to your system.

Here the CHARMM library

http://mackerell.umaryland.edu/charmm_ff.shtml

Probably there is no a released FF which describe your missing fragment so you need to customize the top file by omology.

I recommend you to spend few days in becoming familiar with the tcl scripting and to follow tutorials with non standard fragment and after that all your doubts will be more clear.

Best

Dear Paolo, Thank you for your reply. My protein-DNA system does not contain any non-standard amino acids as well as DNA....

I said non-standard fragments (ie atoms connection like could be C7 in your THY)

C7 comes from Thymine (DNA) and it should be standard fragment - was for AMBER and GROMACS software packages ....

Do you know maybe a software that I could use to correctly prepare my DNA for psfgen?

Dear Urszula, if you look in the top_all36_na.rtf at the line called RESI THY you can see that there is no C7 atom. So you have to understand if C7 (this is the name in the PDB) needs to be renamed to find a correspondece in the top_36 file or, if it is not explicit present, you must insert manually the missing parameters.

We are talking about CHARMM FF.

Another option is to use AMBER and through AmberTools suite you can build your parameters file using Xleap or Tleap. At this point you can run your MD with NAMD with the AMBER keywords:

http://www.ks.uiuc.edu/Research/namd/2.9/ug/node13.html

I hope I was clear

Thank you Paolo,

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