Please keep your messages in your own thread, without using other
people's threads.
It avoids confusion now, and makes answers more findable for the archives.
Bill
On 6/28/17 10:30 AM, Rana Rehan Khalid wrote:
> Actually i am confusing about these part of commands can you guide me how i
> can produce file that use in these command
>
>
> HEM = loadmol2 hem.mol2 >>>> HEME coordinate file
> CYP = loadmol2 cyp.mol2 >>>> CYS (rename this CYS to CYM) residue to make
> coordinate bond with HEME
> 2j2 = loadpdb CYP2J2.pdb >>>> protein system
> set 2j2.460.28 element "Fe"
> bond 2j2.460.28 2j2.405.8 >>>> making the bond between HEME and CYS #BOND
> CYS-S to HEM-FE
> set 2j2.405 connect0 2j2.405.1
> set 2j2.405 connect1 2j2.405.9
> bond 2j2.404.9 2j2.405.1 #BOND CYS to the protein (new CYP residue)
> bond 2j2.405.9 2j2.406.1 #As above
> addions 2j2 Na+ 0
> solvateoct 2j2 TIP3PBOX 10
> saveamberparm 2j2 CYP2J2_FE_box.prmtop CYP2J2_FE_box.inpcrd
>
>
> regards
>
> On Wed, Jun 28, 2017 at 1:27 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> Are you seeing any error messages? Do you have write permission in the
>> directory the files are supposed to appear in?
>>
>> Bill
>>
>>
>> On 6/28/17 10:19 AM, Núbia Prates wrote:
>>> Hello,
>>>
>>>
>>> I am using the following command to generate some files during
>> equilibrate step:
>>>
>>> sander -O -i equi_10.in -p complex.top -c heat.rst -r equi_10.rst -o
>> equi_10.out -x equi_10.mdcrd -ref heat.rst
>>>
>>> The problem is that sander do not write the "equi_10.rst" and "
>> equi_10.mdcrd" files.
>>> Can you help me with that?
>>>
>>>
>>> Regards
>>>
>>> Nubia
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
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>>
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Received on Wed Jun 28 2017 - 11:00:05 PDT
