Now I converted the pdb file by using charmmlipid2amber.py (mentioned in amber tutorial “
http://ambermd.org/tutorials/advanced/tutorial16/”). Now when I load the pdb I got this messages:
Created a new atom named: CAY within residue: .R<NARG 2>
Created a new atom named: HY1 within residue: .R<NARG 2>
Created a new atom named: HY2 within residue: .R<NARG 2>
Created a new atom named: HY3 within residue: .R<NARG 2>
Created a new atom named: CY within residue: .R<NARG 2>
Created a new atom named: OY within residue: .R<NARG 2>
Created a new atom named: HN within residue: .R<NARG 2>
Created a new atom named: HB1 within residue: .R<NARG 2>
Created a new atom named: HG1 within residue: .R<NARG 2>
Created a new atom named: HD1 within residue: .R<NARG 2>
Created a new atom named: HN within residue: .R<LEU 3>
Created a new atom named: HB1 within residue: .R<LEU 3>
Created a new atom named: HN within residue: .R<TRP 4>
Created a new atom named: HB1 within residue: .R<TRP 4>
Created a new atom named: HN within residue: .R<ARG 5>
Created a new atom named: HB1 within residue: .R<ARG 5>
Created a new atom named: HG1 within residue: .R<ARG 5>
Created a new atom named: HD1 within residue: .R<ARG 5>
Created a new atom named: HN within residue: .R<LEU 6>
Created a new atom named: HB1 within residue: .R<LEU 6>
Created a new atom named: HN within residue: .R<LEU 7>
Created a new atom named: HB1 within residue: .R<LEU 7>
Created a new atom named: HN within residue: .R<TRP 8>
Created a new atom named: HB1 within residue: .R<TRP 8>
Created a new atom named: HN within residue: .R<ARG 9>
Created a new atom named: HB1 within residue: .R<ARG 9>
Created a new atom named: HG1 within residue: .R<ARG 9>
Created a new atom named: HD1 within residue: .R<ARG 9>
Created a new atom named: HN within residue: .R<LEU 10>
Created a new atom named: HB1 within residue: .R<LEU 10>
Created a new atom named: HN within residue: .R<TRP 11>
Created a new atom named: HB1 within residue: .R<TRP 11>
Created a new atom named: HN within residue: .R<ARG 12>
Created a new atom named: HB1 within residue: .R<ARG 12>
Created a new atom named: HG1 within residue: .R<ARG 12>
Created a new atom named: HD1 within residue: .R<ARG 12>
Created a new atom named: HN within residue: .R<ARG 13>
Created a new atom named: HB1 within residue: .R<ARG 13>
Created a new atom named: HG1 within residue: .R<ARG 13>
Created a new atom named: HD1 within residue: .R<ARG 13>
Created a new atom named: HN within residue: .R<LEU 14>
Created a new atom named: HB1 within residue: .R<LEU 14>
Created a new atom named: HN within residue: .R<TRP 15>
Created a new atom named: HB1 within residue: .R<TRP 15>
Created a new atom named: HN within residue: .R<ARG 16>
Created a new atom named: HB1 within residue: .R<ARG 16>
Created a new atom named: HG1 within residue: .R<ARG 16>
Created a new atom named: HD1 within residue: .R<ARG 16>
Created a new atom named: HN within residue: .R<LEU 17>
Created a new atom named: HB1 within residue: .R<LEU 17>
Created a new atom named: HN within residue: .R<LEU 18>
Created a new atom named: HB1 within residue: .R<LEU 18>
Created a new atom named: HN within residue: .R<ARG 19>
Created a new atom named: HB1 within residue: .R<ARG 19>
Created a new atom named: HG1 within residue: .R<ARG 19>
Created a new atom named: HD1 within residue: .R<ARG 19>
Created a new atom named: NT within residue: .R<ARG 19>
Created a new atom named: HNT within residue: .R<ARG 19>
Created a new atom named: CAT within residue: .R<ARG 19>
Created a new atom named: HT1 within residue: .R<ARG 19>
Created a new atom named: HT2 within residue: .R<ARG 19>
Created a new atom named: HT3 within residue: .R<ARG 19>
One sided connection. Residue: TP3 missing connect0 atom.
total atoms in file: 41734
Leap added 52 missing atoms according to residue templates:
52 H / lone pairs
The file contained 62 atoms not in residue templates
Then when iwant to save the topology and coordinate files, I got this error:Checking Unit.
WARNING: The unperturbed charge of the unit: 1.000000 is not zero.
FATAL: Atom .R<NARG 2>.A<CAY 27> does not have a type.
FATAL: Atom .R<NARG 2>.A<HY1 28> does not have a type.
FATAL: Atom .R<NARG 2>.A<HY2 29> does not have a type.
FATAL: Atom .R<NARG 2>.A<HY3 30> does not have a type.
FATAL: Atom .R<NARG 2>.A<CY 31> does not have a type.
FATAL: Atom .R<NARG 2>.A<OY 32> does not have a type.
FATAL: Atom .R<NARG 2>.A<HN 33> does not have a type.
FATAL: Atom .R<NARG 2>.A<HB1 34> does not have a type.
FATAL: Atom .R<NARG 2>.A<HG1 35> does not have a type.
FATAL: Atom .R<NARG 2>.A<HD1 36> does not have a type.
FATAL: Atom .R<LEU 3>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 3>.A<HB1 21> does not have a type.
FATAL: Atom .R<TRP 4>.A<HN 25> does not have a type.
FATAL: Atom .R<TRP 4>.A<HB1 26> does not have a type.
FATAL: Atom .R<ARG 5>.A<HN 25> does not have a type.
FATAL: Atom .R<ARG 5>.A<HB1 26> does not have a type.
FATAL: Atom .R<ARG 5>.A<HG1 27> does not have a type.
FATAL: Atom .R<ARG 5>.A<HD1 28> does not have a type.
FATAL: Atom .R<LEU 6>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 6>.A<HB1 21> does not have a type.
FATAL: Atom .R<LEU 7>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 7>.A<HB1 21> does not have a type.
FATAL: Atom .R<TRP 8>.A<HN 25> does not have a type.
FATAL: Atom .R<TRP 8>.A<HB1 26> does not have a type.
FATAL: Atom .R<ARG 9>.A<HN 25> does not have a type.
FATAL: Atom .R<ARG 9>.A<HB1 26> does not have a type.
FATAL: Atom .R<ARG 9>.A<HG1 27> does not have a type.
FATAL: Atom .R<ARG 9>.A<HD1 28> does not have a type.
FATAL: Atom .R<LEU 10>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 10>.A<HB1 21> does not have a type.
FATAL: Atom .R<TRP 11>.A<HN 25> does not have a type.
FATAL: Atom .R<TRP 11>.A<HB1 26> does not have a type.
FATAL: Atom .R<ARG 12>.A<HN 25> does not have a type.
FATAL: Atom .R<ARG 12>.A<HB1 26> does not have a type.
FATAL: Atom .R<ARG 12>.A<HG1 27> does not have a type.
FATAL: Atom .R<ARG 12>.A<HD1 28> does not have a type.
FATAL: Atom .R<ARG 13>.A<HN 25> does not have a type.
FATAL: Atom .R<ARG 13>.A<HB1 26> does not have a type.
FATAL: Atom .R<ARG 13>.A<HG1 27> does not have a type.
FATAL: Atom .R<ARG 13>.A<HD1 28> does not have a type.
FATAL: Atom .R<LEU 14>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 14>.A<HB1 21> does not have a type.
FATAL: Atom .R<TRP 15>.A<HN 25> does not have a type.
FATAL: Atom .R<TRP 15>.A<HB1 26> does not have a type.
FATAL: Atom .R<ARG 16>.A<HN 25> does not have a type.
FATAL: Atom .R<ARG 16>.A<HB1 26> does not have a type.
FATAL: Atom .R<ARG 16>.A<HG1 27> does not have a type.
FATAL: Atom .R<ARG 16>.A<HD1 28> does not have a type.
FATAL: Atom .R<LEU 17>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 17>.A<HB1 21> does not have a type.
FATAL: Atom .R<LEU 18>.A<HN 20> does not have a type.
FATAL: Atom .R<LEU 18>.A<HB1 21> does not have a type.
FATAL: Atom .R<ARG 19>.A<HN 25> does not have a type.
FATAL: Atom .R<ARG 19>.A<HB1 26> does not have a type.
FATAL: Atom .R<ARG 19>.A<HG1 27> does not have a type.
FATAL: Atom .R<ARG 19>.A<HD1 28> does not have a type.
FATAL: Atom .R<ARG 19>.A<NT 29> does not have a type.
FATAL: Atom .R<ARG 19>.A<HNT 30> does not have a type.
FATAL: Atom .R<ARG 19>.A<CAT 31> does not have a type.
FATAL: Atom .R<ARG 19>.A<HT1 32> does not have a type.
FATAL: Atom .R<ARG 19>.A<HT2 33> does not have a type.
FATAL: Atom .R<ARG 19>.A<HT3 34> does not have a type.
Failed to generate parameters
Parameter file was not saved.
On Friday, December 11, 2015 12:43 AM, mohammad r <mohammad.r0325.yahoo.com> 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 12:27 AM, mohammad r <mohammad.r0325.yahoo.com> 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.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> --
>> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
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>>
>>
>>
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>>
>
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Received on Thu Dec 10 2015 - 13:30:06 PST
