dcd file produced with NAMD can be used with AMBER?

From: Rita Cassia (Rita.Cassia_at_gmx.de)
Date: Wed Mar 28 2007 - 04:11:56 CDT

Dear All,

I have done a simulation of an ethanol box (first NVT Ensemble until 300 K; then NPT in order to equilibrate the density). After these simulations, I have got the dcd., coor, vel. files from NAMD.

Then I save the last frame of the simulation by VMD as a pdb file, that I could open in xleap (AMBER). The intention is to solvate a pheo a. molecule, which I have all the parameters from AMBER, in such box. When I opened the pdb file in xleap, the program has accused :

"created a new atom named: H1 within residue ..."
"FATAL: Atom .R<E 28>.A<H5 4> does not have a type."
"Warning: Close contact of 1.042937 angstroms between .R<E 4>.A<O3 8> and .R<E 4>.A<H3 9>"
"check: Errors: 3393 Warnings: 2677"

My question is (sincerely I do hope someone can help me): is there a way to convert the files produced by NAMD (top. files, crd. files; dcd. file) that could be understood by xleap (amber)?

So, if someone has some ideas, please contact me.

Thanks in advance.

Rita Leite

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