Aha! CLA and SOD are not AMBER types, they are CHARMM types. You will
have to change them to "Cl-" and "Na+" in the PDB in order for them to
be recognized.
On 12/10/2015 02:57 PM, mohammad r wrote:
> It can read it but wit these lines for all the residues and atoms:
> Created a new atom named: CLA within residue: .R<CLA 13811>
> Creating new UNIT for residue: CLA sequence: 13812
> Created a new atom named: CLA within residue: .R<CLA 13812>
> total atoms in file: 41734
> Leap added 52 missing atoms according to residue templates:
> 52 H / lone pairs
> The file contained 41387 atoms not in residue templates
> but when I want to save the topology and coordinate files I got this error for all the atoms:
> FATAL: Atom .R<CLA 13810>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 13811>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 13812>.A<CLA 1> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> By the way if you want I can resend the previous mails.
> Thank you, Mohammad.
>
>
>
> On Friday, December 11, 2015 12:01 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>
> 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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--
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 - 13:30:03 PST
