February 2008 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [Dock-fans] How to get the charged mol for the ligand
by Eric Pettersen 04 Feb '08

04 Feb '08

Hi Carlos, There are basically three things you can do: 1) Download the latest daily build and try that. I have been working hard on atom typing for ring systems recently (and am still working on it) and there's a pretty good chance that it will type (and therefore protonate) the phenyl oxygen correctly now. You get a daily build by going to the Chimera home page (www.cgl.ucsf.edu/ chimera) and following the "Daily Builds" link. 2) Directly edit the structure (after adding hydrogens but before adding charges). Control-double-click the oxygen and select "Modify Atom" from the pop-up menu. In the resulting dialog change the element type to O, the geometry to tetrahedral, and the number of bonds to 2. You should also probably change the atom name field to be the same as what the atom's name is. Then click the Change button and the hydrogen will be added. 3) Before doing any processing, change the bond length. Control double-click on the C-O bond and choose "Set Bond Length" from the pop-up menu. Type in a bond length appropriate for a C-O single bond and then run the rest of your processing. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 2, 2008, at 5:19 PM, cpsosa(a)comcast.net wrote: > > Hello, > > We have the opposite problem, our PDB has one oxygen that is part > of a phenyl group and after using addH in Chimera, hydrogen does > not get added to that oxygen. Is there a way to add hydrogen to a > single atom? using Chimera. For Chimera to add a hydrogen to that > O... perhaps making the C-O bond larger. > > Any suggestions? > > Thanks, > > -- > Carlos P. Sosa > > -------------- Original message ---------------------- > From: Eric Pettersen <pett(a)cgl.ucsf.edu> >> I assume this is IMZ from 1rv1? Chimera is adding a proton to the N3 >> nitrogen that it shouldn't. After adding hydrogens and before saying >> OK to the charge calculation, type this command to Chimera's command >> line to delete the extra hydrogen: >> >> del :IMZ@h3 >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >>> I could not get the charges for my molecule (ligand in x-crystal >>> structure). how to do that? >>> I am getting the following error message. >>> I am using chimera to do these funtions. >>> >>> Running ANTECHAMBER command: C:\Program Files\Chimera\bin >>> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp >>> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1\temp >>> \tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 >>> (IMZ) >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >>> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC - >>> f ac -j part >>> (IMZ) >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >>> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff >>> (IMZ) Total number of electrons: 351; net charge: 1 >>> (IMZ) INFO: Number of electrons is odd: 351 >>> (IMZ) Please check the total charge (-nc flag) and spin >>> multiplicity (-m flag) >>> Failure running ANTECHAMBER for residue IMZ >>> >>> >>> Thomas >> >> > > > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: January 31, 2008 12:54:24 PM PST > To: dock-fans(a)docking.org > Subject: Re: [Dock-fans] How to get the charged mol for the ligand > > > I assume this is IMZ from 1rv1? Chimera is adding a proton to the > N3 nitrogen that it shouldn't. After adding hydrogens and before > saying OK to the charge calculation, type this command to Chimera's > command line to delete the extra hydrogen: > > del :IMZ@h3 > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >> I could not get the charges for my molecule (ligand in x-crystal >> structure). how to do that? >> I am getting the following error message. >> I am using chimera to do these funtions. >> >> Running ANTECHAMBER command: C:\Program Files\Chimera\bin >> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp >> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 >> \temp\tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 >> (IMZ) >> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC >> -f ac -j part >> (IMZ) >> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff >> (IMZ) Total number of electrons: 351; net charge: 1 >> (IMZ) INFO: Number of electrons is odd: 351 >> (IMZ) Please check the total charge (-nc flag) and spin >> multiplicity (-m flag) >> Failure running ANTECHAMBER for residue IMZ >> >> >> Thomas > > > _______________________________________________ > Dock-fans mailing list > Dock-fans(a)docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > >

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Aligning two residues same name
by Francesco Pietra 04 Feb '08

04 Feb '08

Task: compare/align a single-residue molecule before docking (naked molecule, mol2 or pdb file) with same residue as ligand in a protein after docking/MD (pdb file of a snapshot for complex embedded in a bilayer membrane). Should I change the residue name in one of the two models? Same name poses to me problems. Or there is a direct way? Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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Fwd: Aligning two residues same name
by Francesco Pietra 04 Feb '08

04 Feb '08

Changing residue name works. Deleted membrane, saved pdb without membrane. Loaded the two models. Command line: match :XXX :YYY How to put the difference in quantitative terms (rmsd)? Thanks francesco --- Francesco Pietra <chiendarret(a)yahoo.com> wrote: > Date: Mon, 4 Feb 2008 06:59:25 -0800 (PST) > From: Francesco Pietra <chiendarret(a)yahoo.com> > Subject: Aligning two residues same name > To: chimera <chimera-users(a)cgl.ucsf.edu> > > Task: compare/align a single-residue molecule before docking (naked molecule, > mol2 or pdb file) with same residue as ligand in a protein after docking/MD > (pdb file of a snapshot for complex embedded in a bilayer membrane). Should I > change the residue name in one of the two models? Same name poses to me > problems. Or there is a direct way? > Thanks > francesco pietra > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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Permission to use Chimera created image
by Seymour Yang 02 Feb '08

02 Feb '08

Hi, I wish to obtain permission to use one or two of the virus images shown on your Chimera image gallery (Semliki forest Virus and Sindbis Virus). We are writing a feature article about 3D molecular imaging and would like to include some Chimera images. May I ask whom to contact regarding permission and obtaining higher resolution files? Hope you can help. Seymour Seymour Yang Producer - Science Feature Stories Email: seymour(a)sciencephoto.com Website: www.sciencephoto.com Blog:http://sciencephoto.blogspot.com/

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Loading prmtop/mdcrd with partial workout
by Francesco Pietra 01 Feb '08

01 Feb '08

I am experiencing difficulties with Amber ptraj in removing solvent/lipid/box (i.e., unexpected problems of prmtop fitting after that, though I used a prmtop before creating solvent/lipid/box). Otherwise, I have memory problems with Chimera in loading such an extensive MD (many ns, in various coordinate files) with all the burden of solvent/lipid/box. My question: is that feasible with Chimera to load a coordinate file, remove solvent and lipid, load a second coordinate file, remove solvent and lipid, and so on for all coordinate files? Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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screening
by snoze pa 01 Feb '08

01 Feb '08

In continuation to my previous question, Is it possible to use chimera in virtual screening?

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