Hello Aditya
Sorry I aslo dont have.
You go through the tutorial
http://ambermd.org/tutorials/basic/tutorial4b/
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_five/create_prmtop.htm
load prepin,frcmod download from amber parameter database and then saveoff .lib
file
Good luck
> 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.
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Fri Feb 18 2011 - 01:00:02 PST
