If pdb4amber does not do what you want, please report here:
https://github.com/Amber-MD/pdb4amber/issues
thanks
Hai
On Wed, Jul 26, 2017 at 12:14 AM, Akshar Sharma <sarojakshar.gmail.com> wrote:
> I'll try running the pdb file through pdb4amber.
> I've been looking at tutorials B4 and B5 because I'll eventually have to do
> force field calculations, but first I have to get the proper pdb for my
> molecule.
>
> Thank you so much for your help!
>
> On Wed, Jul 26, 2017 at 5:32 AM, David Case <david.case.rutgers.edu> wrote:
>
>> On Fri, Jul 21, 2017, Akshar Sharma wrote:
>>
>> > I did try that, but it seems that in order to use addresidue() , I would
>> > have to define a residue library for my special residues in the directory
>> > $AMBERHOME/dat/reslib which I'm not sure how to do...
>> > Is there any way to use addresidue without doing this?
>> > Otherwise, how do I define a residue library (is there any book or
>> website
>> > that could teach me how to?)
>>
>>
>> If you just need the coordinates (say in PDB format, for some other
>> application), things should be much simpler. If the residue numbers
>> are not correct, try running the pdb file you get through pdb4amber. You
>> will
>> have to make sure that your input pdb file has TER cards after each strand
>> (aka
>> chain).
>>
>> If you need to carry out force field calculations, you'll have to learn how
>> to make libraries for modified residues. See, e.g. tutorials B4 and B5.
>> But
>> you might not need NAB for that...
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 25 2017 - 21:30:03 PDT
