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
_______________________________________________
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Received on Fri Feb 09 2018 - 08:30:02 PST
