Have you studied the manual and tutorials to see what it takes to make a
pdb ready to load, with all the residue libraries you need, and the
correct atom names in the pdb? Your problems could be addressed by some
reading there.
Regards,
Bill
On 12/10/15 9:06 PM, mohammad r wrote:
> Hi David,
> This the commands which I used:> source leaprc.ff14SB> loadAmberParams frcmod.ionsjc_tip3p> mol=loadpdb solvated.pdb
> And then I tried to save parameters. CLA is Chloride.By the way, when I save a pdb or parameter files in tleap, it automatically add hydrogen to all the residues. Is there any way to make the tleap not to do that?
>
>
>
>
> On Friday, December 11, 2015 1:04 AM, David A Case <david.case.rutgers.edu> wrote:
>
>
> On Thu, Dec 10, 2015, mohammad r wrote:
>
>> Created a new atom named: CLA within residue: .R<CLA 13811>
>> Creating new UNIT for residue: CLA sequence: 13812
> You must load an Amber library for the CLA unit. I'm assuming you have not
> done this, although you fail to mention which libraries you *did* load.
>
> What is CLA? Chloride? (It appears to be a residue with only a single atom.)
> You must make sure that the residue and atom names in the input pdb file match
> those in the Amber libraries that you load. In many cases, this will require
> manual editing of the pdb files.
>
> (Note that many uncertainties would be resolved if you posted all of the
> commands you gave to tleap, not just the error messages.)
>
> ...dac
>
>
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Received on Fri Dec 11 2015 - 00:30:03 PST
