AMBER: pdb file produced by vmd

From: Rita Cassia <>
Date: Mon, 26 Mar 2007 18:04:19 +0200

Dear All,

after making simulations, using NAMD, for an ethanol box, created in xleap (first : NVT simulations and then NPT, in order to correct the density); I had got the dcd, coor., vel. , etc. files produced by NAMD. After loading the top. file (from leap) and the coor. and visualizing the simulation (dcd file), I saved the last frame in VMD as a pdb file.

Then, I opened xleap, loaded source leaprc.gaff plus the lib. file from the ethanol box and opened the pdb file. I had got such messages:
a) "unknown residue: E number : 1 type: Nonterminal";
"created a new atom name: CT1 within residue : .R<E 1>"

b) "Fatal: Atom .R<E 35>.A<H 26> does not have a type"

c) "Warning: close contact of 1.14 A between .R<E116>.A<CT1 1> and .R<E116>.A<H4 3>"

My question is: after looking at a tutorial "", where a MD simulation on DNA in mixed water-ethanol solvent had been done, I have seen that, after performing 4 steps in order to equilibrate the ethanol box, there were commands that could create pdb files from the output sander files.

Is there a similar way that someone , who has made simulations with NAMD and produced dcd and coor files, could also produce pdb files and all the necessary ones (from the namd output files) in leap. What I need to do is, after equilibrating the box, to solvate chromophore complexes in such boxes.

I would be very glad if someone could give me some ideas.

Thanks in advance.

Rita Leite
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Received on Wed Mar 28 2007 - 06:07:27 PDT
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