Re: combine.tcl

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Nov 21 2006 - 22:44:51 CST

combine.tcl is for deleting the lipids overlapping the protein.

Annalisa, Could you post the topology file you use as well as your
version of the combine.tcl script?

On Nov 21, 2006, at 3:12 PM, Peter Freddolino wrote:

> Hi Annalisa,
> did you delete the lipids close to your protein? The errors you're
> getting usually indicate that you have atoms too close to each other,
> which can easily happen if you have lipids or water that are close to
> your protein and weren't removed.
> Also, what is the combine.tcl script you mention?
> Peter
>
> Annalisa Marsico wrote:
>> Hi all,
>> I am trying to run a simulation of rhodopsin in membrane.
>> After building the membrane and inserting the protein into the
>> membrane I saved both coordinates of membrane and protein.
>> When I run the combine.tcl script I get the following error messages
>> in the log file (my suspicion is that this has something to do with
>> vmd version that I use, that is vmd 1.8.4):
>>
>> Info) VMD for LINUX, version 1.8.4a22 (October 11, 2005)
>> Info) http://www.ks.uiuc.edu/Research/vmd/
>> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
>> Info) Please include this reference in published work using VMD:
>> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
>> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
>> Info) -------------------------------------------------------------
>> Info) Multithreading available, 2 CPUs detected.
>> on
>> 1.4.3
>> reading topology file
>> /home/bioinf/annalisa/Rhodopsin_simul/top27rodlip.inp
>>
>>>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
>>>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
>> from
>>>>>>>>>> CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
>> and
>> \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
>> \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
>> Alexander D. MacKerell Jr.
>> August 1999
>> All comments to ADM jr. email: alex,mmiris.ab.umd.edu
>> telephone: 410-706-7442
>>
>> Created by CHARMM version 27 1
>> *ERROR! Explicit exclustions not supported, atom ignored.
>> ERROR! Explicit exclustions not supported, atom ignored.*
>> reading topology file
>> /home/bioinf/annalisa/Rhodopsin_simul/retinal_top.inp
>>
>> Created by CHARMM version 22 1
>> reading structure from psf file
>> /home/bioinf/annalisa/Rhodopsin_simul/membrane.psf
>>
>> reading coordinates from pdb file
>> /home/bioinf/annalisa/Rhodopsin_simul/membrane.pdb
>> reading structure from psf file
>> /home/bioinf/annalisa/Rhodopsin_simul/1u19_new.psf
>>
>> reading coordinates from pdb file
>> /home/bioinf/annalisa/Rhodopsin_simul/1u19_new_new.pdb
>>
>> temp
>> Info: writing psf file temp.psf
>> total of 43415 atoms
>> total of 40516 bonds
>> total of 68271 angles
>> total of 92122 dihedrals
>> total of 2112 impropers
>> Info: psf file complete.
>> Info: writing pdb file temp.pdb
>> Info: pdb file complete.
>> Info) Using plugin pdb for structure file temp.pdb
>> Info) Using plugin pdb for coordinates from file temp.pdb
>> Info) Determining bond structure from distance search ...
>> *ERROR) MolAtom 32514: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 10278: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 5363: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 42101: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 6837: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 40429: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 18336: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 40723: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 35120: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 40723: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 19808: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 19806: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 18336: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 6165: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 7003: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 19956: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 19177: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 20747: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 5497: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 6300: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 33660: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 19270: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 39303: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 20361: Exceeded maximum number of bonds (8).
>> ERROR) MolAtom 7523: Exceeded maximum number of bonds (8).
>> ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps
>> atom coordinates are in the wrong units?
>> ERROR) BaseMolecule: Silencing bonding error messages.*
>> Info) Finished with coordinate file temp.pdb.
>> Info) Analyzing structure ...
>> Info) Atoms: 43415
>> Info) Bonds: 56999
>> Info) Residues: 4070
>> Info) Waters: 2893
>> *ERROR) Residue exceeded maximum number of bonds (4).
>> ERROR) Residue exceeded maximum number of bonds (4).
>> ERROR) Residue exceeded maximum number of bonds (4).
>> ERROR) Residue exceeded maximum number of bonds (4).
>> ERROR) Residue exceeded maximum number of bonds (4).
>> ERROR) Residue exceeded maximum number of bonds (4).
>> ERROR) Residue exceeded maximum number of bonds (4).
>> ERROR) Residue exceeded maximum number of bonds (4).
>> *
>>
>>
>>
>> I have no clue how to handle this errors. Any suggestion or help is
>> really appreciated!!
>> Thanks
>> Annalisa

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