AMBER Archive (2008)

Subject: Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap

From: Jeff Schwinefus (schwinef_at_stolaf.edu)
Date: Fri Jul 11 2008 - 11:41:21 CDT

Thank you both for your help. rdparm does indeed indicate the correct
vdw parameters in my prmtop file. Interestingly, I found this in the
first part of my leap.log file:

> parm99 = loadamberparams parm99.dat
Loading parameters: /home/apps/amber9/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
(UNKNOWN ATOM TYPE: HZ)
(UNKNOWN ATOM TYPE: NY)
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: Li)
(UNKNOWN ATOM TYPE: IP)
(UNKNOWN ATOM TYPE: K)
(UNKNOWN ATOM TYPE: Rb)
(UNKNOWN ATOM TYPE: Cs)
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: IB)
(UNKNOWN ATOM TYPE: LP)

It appears leaprc.ff99 does indeed not list these under addatomtypes.
Thanks again.

Jeff

David A. Case wrote:
> On Thu, Jul 10, 2008, Thomas Cheatham III wrote:
>
>> ...
>>
>>> (UNKNOWN ATOM TYPE: Li+)
>>> (UNKNOWN ATOM TYPE: Na+)
>>> (UNKNOWN ATOM TYPE: K+)
>>> (UNKNOWN ATOM TYPE: Rb+)
>>> (UNKNOWN ATOM TYPE: Cs+)
>>> (UNKNOWN ATOM TYPE: F-)
>>> (UNKNOWN ATOM TYPE: Cl-)
>>> (UNKNOWN ATOM TYPE: Br-)
>>> (UNKNOWN ATOM TYPE: I-)
>>>
>
> I think you just need to have the appropriate lines in the addAtomTypes
> lines in leaprc files. And I don't think the lack of such lines causes
> any problems, but it is good to double-check that.
>
> ...dac
>
>

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