[gmx-users] psf 2 top

[Florian Haberl]

Hi,

On Wednesday, 5. September 2007 14:14, andrea carotti wrote:
> Hi all,
> I've performed my MD simulations using the charmm FF and NAMD (so
> pdb,psf and dcd files). Now i would like to use the great GMX analysis
> tools. I've successfully converted the dcd file in trr (using catDCD).
> Now the next step I'd like to do is the psf to top conversion. I've seen
> on the vmd site that a top2psf script is present but it not do the
> reverse conv that i need. I would prefer to not pass through pdbs.I
> would like to do this to not loose corrispondences of atoms and to not
> miss parameters for not typical residues that I'm using (like
> phosphrilated serines).
> Is there someone that could help me on this topic?

Easiest solution (also fastest):

Convert your files to multiple pdb, change residue names of HIS HIP (if  they 
are not standard) 

than: dump first frame of this file as a reference pdb file

convert the multiple pdb file to an xtc file

trjconv -f your_multiple_pdb_from_namd.pdb -f 
your_multiple_pdb_from_namd.pdb -dump 0 -o 0.pdb

trjconv -s 0.pdb -f your_multiple_pdb_from_namd.pdb -o protein.xtc

Than you can run at least g_covar and show things, 

g_dist for example only works if you got an valid .tpr file.

> Thanks in advance
> Andrea
>
>
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Greetings,

Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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