[gmx-users] TPO and SEP is is added in residue.date

Justin Lemkul jalemkul at vt.edu
Mon May 9 14:16:48 CEST 2016

On 5/9/16 12:46 AM, Mehreen Jan wrote:
> respected sir!
> thank you for your response!
> version 5.0.7
> forcefield 43a1p
> Question 1
> i run  phosphorylated simulation 10ns result are good known i want to extend my simulation to 20ns the problem is at 11ns i generate PDB i am shocked to see that my TPO and SEP is no more in the pdb. structure is breakdown :( i have no idea what happen to my pdb :( :(
> 1) have added these residues to residuetypes.dat
> i am  saving "Protein" when selecting output from trjconv. because it it is protein domain
> command to extend:
> convert-tpr -s  md_0_1.tpr -extend 1000 -o next1.tpr
> mdrun -s next1.tpr -cpi md_0_1.cpt
> to combine xtc command:
> trjcat -f md_0_1.xtc next1.xtc next2.xtc -o concat.xtc -cat
> to generate PDB:
> trjconv -s md_0_1.tpr -f md_0_1.xtc -o time_11000ps.pdb -dump 11000
> and when i open PDB TPO and SEP is disappear from PDB and structure is break down.

If your residuetypes.dat did not contain SEP and TPO as Protein when you created 
your .tpr file, and in the even that you only chose Protein to be saved in your 
.xtc file, those coordinates are never written and you'll have to start the 
simulation over if you want them to be present.  Adding SEP and TPO to 
residuetypes.dat only when trying to execute trjconv will not help in this case. 
  I'm guessing a bit because you haven't provided your .mdp files, but this is 
the most likely case.  You can use gmx check to verify the contents of the .xtc 
files - the number of atoms will tell you whether or not you're saving 
everything you think you did.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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