AMBER Archive (2008)

Subject: Re: AMBER: AddIons approach

From: Germain Vallverdu (germain.vallverdu_at_lcp.u-psud.fr)
Date: Fri Oct 10 2008 - 06:23:00 CDT

Hello

In the leaprc file the good instruction may be :

addIons nmb Na+ 0
or
addIons nmb Cl- 0

insted of

addIons nmb Na 14 Cl 15

Germain

http://www3.interscience.wiley.com/journal/45001708/abstract?CRETRY=1&SRETRY=0

Carlos Simmerling a écrit :
> what does the leap.log file say?
>
>
>
>
> On Fri, Oct 10, 2008 at 7:13 AM, parul sharma <sharmaparul7373_at_gmail.com> wrote:
>
>> Dear Amber users,
>>
>> The problem i am facing is very strange, would be really thankful if you
>> could help me out with it. I tried to add ions to my peptides in water box,
>> but when i create the pdb after getting the 1000.rst file after sander
>> minimization, it doesn't show any ions in it.
>>
>> The leaprc looks like:
>>
>> source leaprc.ff96
>> loadAmberParams frcmod.WAT
>> nmb = sequence {NGLY ASN LEU TRP ALA THR GLY HIS PHE MET NHE}
>> solvateBox nmb TIP3PBOX 12
>> addIons nmb Na 14 Cl 15
>> saveamberparm nmb nmb.prmtop nmb.prmcrd
>> quit
>>
>> It gave me the crd and top files and i performed sander minimization, got
>> 1000.rst file, and it successfully crated the pdb too, but without ions.
>> Please help me.
>>
>> Kind Regards
>> Parul Sharma
>>
>>
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-- 
Germain Vallverdu
Laboratoire de Chimie Physique
Université Paris Sud 11
germain.vallverdu_at_lcp.u-psud.fr
ma page perso <http://pagesperso.lcp.u-psud.fr/vallverdu/>
01 69 15 30 38 / 06 88 59 08 87
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