Re: FW: Multiplicity of parameters for improper bonds .............. of 1 exceeded.

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Dec 11 2008 - 11:51:15 CST

Hi Vlad,
the multiplicity exceeded error occurs if you have an improper listed
more times in the psf than there were entries for it in the parameter
file (this is to allow for multiple different periodicities). You're
probably using the improper
X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL
                ! adm jr. 3/19/92, from lipid methyl acetate
from the parameter file. You should verify that you didn't accidentally
end up with the corresponding improper listed multiple times in your
topology, and that it doesn't occur multiple times in your psf.

Best,
Peter

CHINDEA Vlad wrote:
> Dear all
>
> Sorry but I forgot to add the subject line.
>
> Regards
>
> ------------------------------------------------------------------------
> From: vchindea_at_hotmail.com
> To: namd-l_at_ks.uiuc.edu
> Subject:
> Date: Thu, 11 Dec 2008 14:12:05 +0200
>
> Hi everybody
>
>
> I am trying to simulate a system composed of a protein and a small
> ligand in a box of water. But immediately after I start the simulation
> I got the following message:
>
>
> Multiplicity of parameters for improper bonds CD CT1 OS OB of 1 exceeded.
>
>
> I am pretty sure that this has something to do with the ‘tampering’ of
> the topology file that I had to do in order to accommodate the small
> ligand, composed of a single aminoacid with NTER and CT1 patches.
> Since both patches cannot by applied on the same residue without
> destroying the molecule I had to change the name of the hydrogens in
> the NTER to HJ1,..,3. Then I tried to do the MD and based on the error
> messages from namd2 I have modeled by analogy all the missing force
> field parameters.
>
>
> Now I am able to simulate the ligand using the modified parameters and
> topology files and also the protein using the original files (par and
> top_all27_protein_lipid_na), but when I try to simulate the protein
> and ligand together with the modified files I got the above mentioned
> error message, which looks quite strange to me since I am not able to
> find any CD CT1 OS OB improper in the parameters file ! Then how come
> is multiplicity exceeded ?
>
>
> Many thanks for your support
>
>
> Best regards
>
> Vlad
>
>
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