Hi,
I believe it should be
Loadamberparams
(Note params, not parms)
--Marc
Sent from my iPhone
> On 10 May 2015, at 19:57, Michael Shokhen <michael.shokhen.biu.ac.il> wrote:
>
> Hi Kenneth,
>
> Thank you for you email and advise.
> I have used the command you suggested:
>
> loadamberparms frcmod.ionsjc_tip3p
>
> Unfortunately xleaps responds with error:
>
> ERROR: syntax error
>
> Michael
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: michael.shokhen.gmail.com
> email: shokhen.mail.biu.ac.il
>
>
> On Sun, May 10, 2015 at 9:35 PM, Kenneth Huang <kennethneltharion.gmail.com>
> wrote:
>
>> Micheal,
>>
>> The general form of the command you're likely looking for is-
>>
>> loadamberparms frcmod.ionsjc_tip3p
>>
>> Usually, you want to load it before you add in your counterions. Note that
>> the above forcefield is just the one that I default to- I believe there's a
>> number of forcefields for different situations.
>>
>> Best,
>>
>> Kenneth
>>
>> On Sunday, May 10, 2015, Michael Shokhen <michael.shokhen.biu.ac.il>
>> wrote:
>>
>>> Dear Amber list members,
>>>
>>> I have on ubuntu linux amber14 and amber tools 15 installed.
>>> Preparing protein by xleap I have faced the error message
>>> (see details below).
>>>
>>> What is a correct xleap command for accounting Cl-
>>>
>>> counter ions that will avoid the error?
>>>
>>>
>>> Thank you,
>>> Michael
>>>
>>>
>>> *xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB*
>>>
>>> *>set default PBRadii mbondi2*
>>>
>>> *>p1 = loadpdb hp.pdb*
>>>
>>> *>addions p1 Cl- 0*
>>>
>>> *>solvateoct p1 TIP3PBOX 15*
>>>
>>> *>saveamberparm p1 hp.prmtop hp.inpcrd*
>>>
>>>
>>>
>>>
>>> *Checking Unit.*
>>>
>>> *Building topology.*
>>>
>>>
>>> *Building atom parameters.*
>>>
>>> *For atom: .R<Cl- 153>.A<Cl- 1> Could not find vdW (or other) parameters
>>> for type: Cl-*
>>>
>>> *Parameter file was not saved.*
>>>
>>>
>>>
>>>
>>> *****************************
>>> Michael Shokhen, PhD
>>> Associate Professor
>>> Department of Chemistry
>>> Bar Ilan University,
>>> Ramat Gan, 52900
>>> Israel
>>> email: michael.shokhen.gmail.com <javascript:;>
>>> email: shokhen.mail.biu.ac.il <javascript:;>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org <javascript:;>
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> --
>> Ask yourselves, all of you, what power would hell have if those imprisoned
>> here could not dream of heaven?
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Received on Sun May 10 2015 - 12:30:02 PDT
