Mohamad,
Why not using leap to solvate your protein directly ?
Using the 'solvatebox' command ...
All the best
Eric
-----Original Message-----
From: mohammad r [mailto:mohammad.r0325.yahoo.com]
Sent: Wednesday, December 09, 2015 2:58 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Charmm-gui conversion
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 Wed Dec 09 2015 - 13:00:03 PST
