Ironically I see frcmod.ionsjc_tip3p that you are using uses Na+ and Cl-.
Nor do I see NA in the other ions frcmods, but lots of Na+.
This is in Amber16, not sure if it has changed with 17.
Not sure why NA and CL were advised as I seem to remember.
Bill
On 5/15/17 9:01 AM, Thakur, Abhishek wrote:
> Hi Dr.Case,
>
>
> I have tried using NA and CL for sodium and chlorine but still similar error persist.
>
>
> FATAL: Atom .R<CL 545>.A<CL 2> does not have a type.
> FATAL: Atom .R<NA 546>.A<NA 3> does not have a type.
> FATAL: Atom .R<NA 547>.A<NA 3> does not have a type.
>
>
> Thanking you,
>
> AT
>
> ________________________________
> From: David A Case <david.case.rutgers.edu>
> Sent: Friday, May 12, 2017 1:33:34 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na
>
> On Thu, May 11, 2017, Thakur, Abhishek wrote:
>> I have been doing
>>
>> tleap -s -f leaprc.ff14SB.ORIG
>> source leaprc.gaff
>> loadamberparams UNK.frcmod
>> loadoff UNK.lib
>> Na = loadmol2 Na.mol2
>> Cl = loadmol2 Cl.mol2
>> R_config = loadpdb C8_2.pdb
>> solvateBox R_config TIP3PBOX 10
>> charge R_config
>> addIons R_config Cl- 2
>> loadAmberParams frcmod.ionsjc_tip3p
>> saveamberparm R_config C8.prmtop C8.inpcrd
>> savepdb R_config complex.pdb
>> quit
> OK: you are rolling your own commands, and are pretty much on your own
> to see what is going wrong. Consider using standard leaprc files (e.g.
> leaprc.protein.ff14SB, leaprc.water.tip3p).
>
> I note that you called chloride "Cl" in the loadmol2 command, but called
> it "Cl-" in the addIons command. Look carefully at the leap.log file to
> see exactly what is going on.
>
> Here's my best guess: you get the error for "Na" because the Amber libraries
> recognize "NA" and "Na+" (for backward compatibility), but don't have any
> entries for "Na". There was no error for chloride because of the above typo
> in the addIons command. Easiest fix is probably to edit your pdb file
> and use "NA" and "CL" for sodium and chloride ions.
>
> ....dac
>
>
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Received on Mon May 15 2017 - 12:00:03 PDT
