> Message: 12
> Date: Tue, 28 Jun 2016 10:10:19 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Hidden parameters for tleap
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20160628141019.GB1586.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Tue, Jun 28, 2016, Lea Natalia Toledo Carvajal wrote:
>>
>> I work in the setup of a metaloprotein (Cu+2), using the V.15 of
>> AmberTools.
>> For this system fortunately exist published the Amber parameters. But,
>> when tleap read:
>>
>> > loadamberparams *.frcmod
>>
>> (file that include some of these special parameters), there are 3 that
>> don't read.
>
> You can use the "desc" command in tleap to see what has been loaded. Here
> is what I get, when loading your file:
Thanks for your prompt response.
>
> ===========================================================================
>> y = loadAmberParams example.frcmod
> Loading parameters: ./example.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> Remark line goes here
> Unknown keyword: Cu+2-Omu2- in parameter file. Perhaps a format error?
> Unknown keyword: Omu2-Cu+2- in parameter file. Perhaps a format error?
> Unknown keyword: cc-na-Cu+2 in parameter file. Perhaps a format error?
> Unknown keyword: c2-na-Cu+2 in parameter file. Perhaps a format error?
> Unknown keyword: Cu+2-Omu2- in parameter file. Perhaps a format error?
> Unknown keyword: Cu+2-Omu2- in parameter file. Perhaps a format error?
> Unknown keyword: Omu2-Cu+2- in parameter file. Perhaps a format error?
>> list
Exactly, this format error is in relation with the "space" between the
second and third atom that define the angle. In the attached file
mix.frcmod.txt , a later version (sorry by the extensión .txt, gmail
had troubles with the .frcmod), this was apparently solved (checking
the leap.log.txt, attached), but the parameters still are
unrecognisable for tleap.
> y
>> desc y
> PARMSET
> --Atoms
> --None
> --Bonds
> --None
> --Angles
> Cu+2 - NB - V Kt= 125.00 T0= 10.00 Desc:
> NB - Cu+2 - na Kt= 109.50 T0= 0.01 Desc:
> NB - Cu+2 - NB Kt= 109.50 T0= 0.01 Desc:
> NB - Cu+2 - Omu2 Kt= 109.50 T0= 0.01 Desc:
> CR - NB - Cu+2 Kt= 127.00 T0= 10.00 Desc:
> O - C - n2 Kt= 80.00 T0= 122.90 Desc:
> CX - C - n2 Kt= 70.00 T0= 116.60 Desc:
> H - N - c Kt= 50.00 T0= 118.04 Desc:
> CX - N - c Kt= 70.00 T0= 116.60 Desc:
> O - C - n2 Kt= 80.00 T0= 122.90 Desc:
> NB - Cu+2 - na Kt= 109.50 T0= 0.01 Desc:
> Omu2 - Cu+2 - na Kt= 109.50 T0= 0.01 Desc:
> --Torsions
> --None
> --Impropers
> --None
> --HBonds
> --None
> --Nonbonded Edits
> --None
> ===========================================================================
>
> So: do you see any "unknown keyword" errors? Have you entered (perhaps via
> a leaprc file) the requisite AddAtomType commands (esp. for type Omu2)?
I believed that was enough that in the corresponding new topology
files (in this case o2.lib or Cup.lib) were specified these new atom
types, and then (just with this information) tleap could relate it to
the parameters file (mix.frcmod), which include the parameters for the
coordinated Cu+2, the Omu2 type oxygen and the others. So, I am wrong,
right? But, why tleap don't have problem with the bond parameters, in
which also are present this new atom types? I am sorry, this is my
first system in Amber and I don't know about this command
(AddAtomType). In which part it must be included, in the input1_leap
(attached also) that reads tleap? seems logical.
>
>> Others similar warning message were solved adjusting the order of the
>> alert with the sequence in which read the parameters in the *.frcmod
>> file and work, but in this case this solution does not work.
>
> I can't follow the above sentence: what does "adjust the order of the alert
> with the sequence" mean--can you give an example?
Yes;
Omitting that need the new command, tleap read mix.frcmod file without
problem if the parameters are included in the same order as they
appears in the warning alerts, but, for example if the alert mention
the next:
Could not find angle parameter: CV - NB -Cu+2
Could not find angle parameter: NB - Cu+2 -na
Could not find angle parameter: NB - Cu+2 -NB
And I include the parameters in this order in the frcmod
NB - Cu+2 -na
NB - Cu+2 -NB
CV - NB -Cu+2
Tleap send again the same warning. But, if I include the parameters in
same order, it works.
Please try to provide a minimal example of a frcmod file that fails, and be
> sure to give the *complete* set of commands that you gave to tleap.
As attached files are the complete files that give form to the system,
which has two copper atoms, two oxygen molecules (coordinating the
cupper atoms) and an unusual tioeter bond between one of the
histidines of coordination , the new HIT residue bonded to the new
Cys, called as CID.
Is true that without the complete files is very difficult to see what
we are doing.
Sincerely thanks for your help.
>
> ...thanks...dac
>
Lea
>
>
> ------------------------------
>
> Message: 13
> Date: Tue, 28 Jun 2016 10:33:03 -0400
> From: Pengfei Li <ambermailpengfei.gmail.com>
> Subject: Re: [AMBER] MCPB
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <331DACE3-5E12-4B06-B7BF-660853321DA3.gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> Hi Fabricio,
>
> I have modified MCPB.py code to make it can work for your case. And I have
> sent an email to your email address about that. Hope it helps.
>
> Kind regards,
> Pengfei
>
>> On Jun 27, 2016, at 3:56 PM, Fabr?cio Bracht <fabracht1.gmail.com> wrote:
>>
>> Hello. I've given up on using MCPB.py, and am trying to use MCPB instead.
>> I need to create a Histidine residue that has a methyl group bonded to
>> the
>> epsilon nitrogen instead of the hydrogen that would be there.
>> So far I've tried to introduce a terminal CH3 with the command:
>>
>> addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.NE2 ag /NAME/CLR/HD1-1/.CD2
>> tr
>> /NAME/CLR/HD1-1/.CE1 165.00
>>
>> This works fine, but the HE2 is still there. There is no command listed
>> on
>> the manual to remove atoms. I could, change the HIE to a HID and transfer
>> the hydrogen to the other nitrogen atom, but the other nitrogen is bonded
>> to the metal ion.
>> Can I replace atoms or even remove them in MCPB?
>>
>> Thank you
>> Fabr?cio
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 14
> Date: Tue, 28 Jun 2016 22:07:23 +0530
> From: Martina Devi <martinadevi2011.gmail.com>
> Subject: [AMBER] prepin to mol2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CA+JOZ38MOWhk5WDpkNT=i+Yc3wat4SQC_9RP5Q2P0fTAhtt=2w.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Amber Users
>
> I gave the following command to convert mol2 file to prepin
>
> OAU=loadmol2 OAU.mol2
> saveamberprep OAU OAU.prep
>
> then I got the following lines:
>
> OAU: connect0 not defined
> OAU: connect1 not defined
> -- Remember to delete improper terms!
>
> Do I have to edit the mol2 file and how do I define connect?
>
> Waiting for help in anticipation.
>
> Thanks in advance
> Martina
>
>
> ------------------------------
>
> Message: 15
> Date: Tue, 28 Jun 2016 22:10:39 +0530
> From: Martina Devi <martinadevi2011.gmail.com>
> Subject: [AMBER] convert mol2 to prepin
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CA+JOZ391Hdxk4FoqAe_uU7+NJZeiKeuzQfmujqykqdo_PqXjHQ.mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Amber Users
>
> I gave the following command to convert mol2 file to prepin
>
> OAU=loadmol2 OAU.mol2
> saveamberprep OAU OAU.prep
>
> then I got the following lines:
>
> OAU: connect0 not defined
> OAU: connect1 not defined
> -- Remember to delete improper terms!
>
> Do I have to edit the mol2 file and how do I define connect? I am attaching
> the mol2 file.
>
> Waiting for help in anticipation.
>
> Thanks in advance
> Martina
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 16
> Date: Tue, 28 Jun 2016 13:18:31 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] prepin to mol2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20160628171831.GA2061.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Tue, Jun 28, 2016, Martina Devi wrote:
>>
>> I gave the following command to convert mol2 file to prepin
>>
>> OAU=loadmol2 OAU.mol2
>> saveamberprep OAU OAU.prep
>>
>> then I got the following lines:
>>
>> OAU: connect0 not defined
>> OAU: connect1 not defined
>
> mol2 files in Amber are intended primarily for ligands that are complete
> molecules (and hence have no covalent connections to external atoms). The
> mol3 format should be used if you wish to use a "mol2-like" format but
> retain connection information that would be needed for things like modified
> residues.
>
> For more info:
>
> http://upjv.q4md-forcefieldtools.org/Tutorial/leap-mol3.php
>
> ...dac
>
>
>
>
> ------------------------------
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1620, Issue 1
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Received on Wed Jun 29 2016 - 03:30:02 PDT
