I can't reproduce your problem. The only other thing I can recommend
is downloading AmberTools 17 and using that.
-Dan
On Fri, Feb 9, 2018 at 11:23 AM, Ahmed Mashaly <mashaly_1988.yahoo.com> wrote:
> Hi again
> This pdb I sent to you was generated by tleap after capping, fixing numbers, etc ....And I used the input you used exactly, even without adding ions but same result!! Kind Regards,Ahmed
>
>
>
> From: Daniel Roe <daniel.r.roe.gmail.com>
> To: Ahmed Mashaly <mashaly_1988.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
> Sent: Friday, February 9, 2018 5:11 PM
> Subject: Re: [AMBER] solvatebox iso error
>
> Yes, although I had to strip hydrogens out of the PDB you supplied -
> some of the names were non-standard and not recognized by the standard
> residue templates. Also your PDB is non-standard (line lengths are too
> short) but leap doesn't seem to worry about that. Did you use my input
> exactly? If you're trying to use the input you posted, I would make
> some changes. Add ions *after* you add solvent, and try using
> addionsrand instead of addions.
>
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
> m = loadpdb noh.pdb
> solvatebox m TIP3PBOX 15.0 iso
> addionsrand m Na+ 42
> addionsrand m Cl- 21
> saveamberparm m test.parm7 test.rst7
> quit
>
> -Dan
>
>
> On Fri, Feb 9, 2018 at 10:51 AM, Ahmed Mashaly <mashaly_1988.yahoo.com> wrote:
>> Hi Dan
>>
>> No, not working. Did it work for you without pdb4amber?
>>
>> Kind Regards,
>> Ahmed
>>
>>
>>
>> ________________________________
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> To: Ahmed Mashaly <mashaly_1988.yahoo.com>; AMBER Mailing List
>> <amber.ambermd.org>
>> Sent: Friday, February 9, 2018 3:02 PM
>>
>> Subject: Re: [AMBER] solvatebox iso error
>>
>> Hi,
>>
>> It seems to work fine for me (see attached). Here's what I did. First
>> I preprocessed with pdb4amber:
>>
>> pdb4amber -i original.pdb -o amber.pdb -y
>>
>> Then I used the following leap input:
>>
>> source leaprc.protein.ff14SB
>> source leaprc.water.tip3p
>> m = loadpdb amber.pdb
>> solvatebox m TIP3PBOX 15.0 iso
>> saveamberparm m test.parm7 test.rst7
>> quit
>>
>> Note that if you don't want to keep the waters in the PDB you can use
>> the '-d' command line flag. Hope this helps,
>>
>> -Dan
>>
>>
>>
>> On Thu, Feb 8, 2018 at 11:32 AM, Ahmed Mashaly <mashaly_1988.yahoo.com>
>> wrote:
>>> And this is the molecule if you wanna
>>> tryhttps://drive.google.com/open?id=17CfGKuPlrEjMbml48EO_ka1rJK2b6SqZ
>>>
>>>
>>> Kind Regards,Ahmed
>>>
>>>
>>>
>>> From: Daniel Roe <daniel.r.roe.gmail.com>
>>> To: Ahmed Mashaly <mashaly_1988.yahoo.com>; AMBER Mailing List
>>> <amber.ambermd.org>
>>> Sent: Thursday, February 8, 2018 1:14 PM
>>> Subject: Re: [AMBER] solvatebox iso error
>>>
>>> Hi,
>>>
>>> What version of AmberTools are you using? Also, can you provide all of
>>> the commands you are giving to leap? I can't seem to reproduce your
>>> error.
>>>
>>> -Dan
>>>
>>>
>>>
>>> On Wed, Feb 7, 2018 at 1:10 PM, Ahmed Mashaly <mashaly_1988.yahoo.com>
>>> wrote:
>>>> Hi
>>>> When I use this command solvatebox prot TIP3PBOX 15 iso
>>>> I have this weird
>>>> boxhttps://drive.google.com/open?id=1xslAwz-0YnDAtfU-u2AZ68JuozKfpzgF
>>>>
>>>> It works fine without iso, but I need a cubic box, not a rectangular
>>>> one!! Kind Regards,Ahmed
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe
>>> Laboratory of Computational Biology
>>> National Institutes of Health, NHLBI
>>> 5635 Fishers Ln, Rm T900
>>> Rockville MD, 20852
>>> https://www.lobos.nih.gov/lcb
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
>>
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 09 2018 - 09:00:03 PST
