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

From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Thu Dec 11 2008 - 06:17:20 CST

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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