I don't see the previous discussion on the archive, so rebooting:
What errors do you get when tleap tries to load the pdb?
Bill
On 12/10/15 12:25 PM, mohammad r wrote:
> Excuse me, can someone help me?
>
>
>
> On Thursday, December 10, 2015 12:01 AM, mohammad r <mohammad.r0325.yahoo.com> wrote:
>
>
> Bill,
> I think I can set a box by set box command. Now the tleap can not read the pdb file.
>
>
> On Wednesday, December 9, 2015 11:37 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>
> By the way, I'm not sure you would have a periodic box if you just
> loadpdb/saveamberparm - unless box reading has been added to loadpdb.
>
> Bill
>
> On 12/9/15 11:58 AM, mohammad r wrote:
>> brian,
>> This the commands which I used:> source leaprc.ff14SB> loadAmberParams frcmod.ionsjc_tip3p> mol=loadpdb solvated.pdb
>> And then I tried to save parameters.
>> Arnoult,I don't understand what you mean, but I want the topology, coordinate and pdb files.
>> By the way I have a question about charmm-gui and unfortunately I cannot register to the charmm mailing list, so ask it here maybe someone can help me. I have a pdb file consisted of a protein and some lipids around it, now i want to solvate it in water by using charmm-gui then convert it to amber to define the forcefields (unfortunately I cannot do it by tleap since I want to solvate it in a box with specific dimensions and tleap does not have a command for it, it just define a box by defining the distance from the molecules), but when I load it in charmm-gui (solvator section) it cannot read the lipids, it wants the topology and coordinate files for them. So I don't know what to do. Also I acetylated the N-terminal and amidated the C-terminal but the charmm-gui can not read them, too.
>>
>>
>>
>> On Wednesday, December 9, 2015 9:57 PM, "Arnoult, Eric [JRDUS]" <EArnoult.its.jnj.com> wrote:
>>
>>
>> Hi Mohammad,
>> In addition to what propose Brian, you might have to do some manual correction in your PDB file.
>> What are the output from leap?
>>
>>
>>
>> -----Original Message-----
>> From: Brian Radak [mailto:brian.radak.accts.gmail.com]
>> Sent: Wednesday, December 09, 2015 11:10 AM
>> To: mohammad r; AMBER Mailing List
>> Subject: Re: [AMBER] Charmm-gui conversion
>>
>> You probably haven't loaded the necessary force field files. Can you post the /exact/ tleap commands?
>>
>> On 12/09/2015 10:02 AM, mohammad r wrote:
>>> Hi everybody,
>>>
>>>
>>> I have generated a water-proteinsystem by charmm-gui (solvator section). I converted the pdb file to amberformat by using this command:” charmmlipid2amber.py –Iinput_structure.pdb [-c substitution_definitions.csv] \ -o output_structure.pdb”(mentioned in amber tutorial “http://ambermd.org/tutorials/advanced/tutorial16/”)but when I load the pdb file in tleap and I want to save the amber top and crdfiles I got the error that some atoms does not have a type in amber. Now I wantto know that is it ok to convert just the pdb file? Is this way of conversioncorrect?
>>>
>>>
>>> Thank you, Mohammad.
>>> _______________________________________________
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>> --
>> Brian Radak
>> Postdoctoral Scholar
>> Gordon Center for Integrative Science, W323A Department of Biochemistry & Molecular Biology University of Chicago
>> 929 E. 57th St.
>> Chicago, IL 60637-1454
>> Tel: 773/834-2812
>> email: radak.uchicago.edu
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Received on Thu Dec 10 2015 - 13:00:04 PST
