Hi Sangita,
I dont have the .lib file instead I have the .prep file that I sent in
the previous mail. If you have any relevent site from where I can get the
.lib file it would be great or else can you sen me the same.
Thank you.
Aditya.
On Fri, Feb 18, 2011 at 11:25 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
> Hello
> You have .lib file and did you loadoff it after loading .frcmod?
> You require .lib file to generate topology and inpcrd for protein having
> ca2+ ion.
> first load .frcmod, .lib then finaly .pdb
> You please again go through the tutorial.
>
> Good Luck
> > Hi all,
> > I am simulating a protein with calcium ion in it. I have removed all
> the
> > hydrogen prior to MD and added using tleap. Then as per the instructions
> at
> > http://enzyme.fbb.msu.ru/Tutorials/Tutorial_2/Sec_1.htm,<
> http://enzyme.fbb.msu.ru/Tutorials/Tutorial_2/Sec_1.htm>I
> > loaded the pdb into a new file and using
> > *loadamberprep metals.prp* command, I added the ion parameter file from
> > http://www.pharmacy.manchester.ac.uk/bryce/amber. Then I saved the pdb
> file
> > but it is showing error like the following
> >
> > mol = loadpdb new.pdb
> > Loading PDB file: ./new.pdb
> > Unknown residue: CA number: 355 type: Terminal/last
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Creating new UNIT for residue: CA sequence: 356
> > Created a new atom named: CA within residue: .R<CA 356>
> > total atoms in file: 5555
> > The file contained 1 atoms not in residue templates
> >
> > I tried but its showing the above error all the time. Kindly help me in
> > resolving the problem. I am attaching the protein PDB, prp, frcmod and
> leap
> > log file for reference.
> >
> > Thank you.
> > Aditya.
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
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>
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Received on Thu Feb 17 2011 - 22:30:02 PST
