[gmx-users] Amber 14SB force-field problem with residue HID
Man Hoang Viet
mhviet at ifpan.edu.pl
Thu Sep 19 16:45:27 CEST 2019
Dear Kenvin,
I am Viet Man, who converted amber14sb to gromacs version. The below link
is my test to compare energy difference of several amber force fields,
gromacs official ones (ff99 and ff99sb) and my converted ones (amber12sb
and ammber14sb). The result showed that my converted force fields as good
as the the GROMACS official ones in term of energy comparison.
http://www.gromacs.org/@api/deki/files/254/=ffA2G_test.pdf
I have not carefully looked at other residues except twenty standard
residues reported in the test. Your problem is similar as the one of HIP
residue, which was posted in GROMACS forum and I have fixed it. You may do
search HIP amber14SB and following the solution to fix the issue of HID.
Otherwise, I will fix this HID issue by this weekend.
Yours sincerely,
Viet Man
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> Today's Topics:
>
> 1. gmx trjorder help (Pandya, Akash)
> 2. Re: Amber 14SB force-field problem with residue HID (Kevin)
> 3. -t option? (Hadi Rahmaninejad)
> 4. Re: -t option? (Mahdi Bagherpoor)
> 5. Tetrahedral Order Parameter (m g)
> 6. Re: Tetrahedral Order Parameter (Dallas Warren)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 18 Sep 2019 12:59:26 +0000
> From: "Pandya, Akash" <akash.pandya.15 at ucl.ac.uk>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] gmx trjorder help
> Message-ID:
> <DB8PR01MB5866E047B9AB9B61898F6A29EB8E0 at DB8PR01MB5866.eurprd01.prod.exchangelabs.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
>
> I used gmx trjorder to order my ligand molecules based on the distance
> from the COM of my protein using the command below:
>
> gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -o ordered.gro
> -nshell nshell1.xvg -b 20000 -e 20000 -na 10 -r 0.5
>
>
>
> I viewed the nshell1.xvg file to see how many ligand molecules were found
> within the shell at a particular time. I know in the gromacs manual it
> says "When an index group of the first n waters is made, the ordered
> trajectory can be used with any GROMACS program to analyze the n closest
> waters". I presume that I can use this for my ligand molecules too.
>
> The problem I have with this is the "ordered" trajectory file contains all
> the ligand molecules even the ones not within the cut-off. Can anybody
> help with this?
>
>
> Akash
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 18 Sep 2019 10:14:13 -0400
> From: Kevin <mcfc1301 at gmail.com>
> To: Gromacs Users List <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Amber 14SB force-field problem with residue
> HID
> Message-ID:
> <CAGcHS=mVnPNExiyOh5OjSqXJWFBtqYiwA+yMfTEC=4eaTVH31Q at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you Justin for your reply. I totally understand the risk of using a
> user-contributed force-field. And that is why I am trying to fix it (and
> test it). Then I rather put my question more as a force-field building
> question, asking how pdb2gmx generates the list of impropers from the
> topology. Hope you could share your experience on this so I could fix it
> by
> myself.
>
> Thanks,
> Kevin
>
> On Thu, 12 Sep 2019 at 19:08, Kevin <mcfc1301 at gmail.com> wrote:
>
>> Dear Users,
>>
>> I have encountered a problem with the Amber force-field downloaded from
>> http://www.gromacs.org/Downloads/User_contributions/Force_fields.
>> Whenever I feed this forcefield to pdb2gmx and get a residue HID for
>> protein topology, it will cause error message: "No default Proper Dih.
>> types". This error can simply be solved by swapping the second and third
>> indices on the line number given with the error message.
>>
>> I tried to dig into the reason behind this error. First, the error line
>> contains atomtypes in a sequence of "CT CC CV NA" which CANNOT be
>> found
>> in ffbonded.itp. Instead, "CT CV CC NA" can be found in ffbonded.itp
>> and
>> I guess that is why my solution worked. However, when I look at the
>> topology of HID, I was confused:
>>
>> [ impropers ]
>> -C CA N H
>> CA +N C O
>> CG CE1 ND1 HD1
>> CG NE2 CD2 HD2
>> ND1 NE2 CE1 HE1
>> ND1 CD2 CG CB
>>
>> Converting from atom name to atomtypes, there is no either "CT CC CV
>> NA" or "CT CV CC NA" in impropers. However, "ND1 CD2 CG CB"
>> is
>> very likely to be the folk just written in a reversed sequence. More
>> interestingly, I gave a try on the Amber ff99*-ILDN forcefield, the HID
>> topology appears to be nearly the same but no error message was
>> produced.
>> The error was always found in the second [dihedrals] block, so I assume
>> it
>> is referred to impropers. That gave me two questions:
>> 1. How does impropers be constructed by pdb2gmx?
>> 2. Why different forcefields seem to give different sequence of
>> atomtypes
>> for imporpers.
>>
>> In fact, Q2 makes absolutely no sense, so I think I must be missing
>> something.
>>
>> Any comment is greatly appreciated.
>>
>> Regards,
>> Kevin
>> The Ohio State University
>>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 18 Sep 2019 11:43:12 -0400
> From: Hadi Rahmaninejad <ha.rahmaani at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] -t option?
> Message-ID:
> <CABZiX_Q6TaxRjP1b12-Ot68CJ7vEd7kZdcc90+7-+J+YzMHvtA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello dear users,
>
> I am going to run a simulation according to a tutorial, but there is an
> option of "-t nvt.cpt" that I don't know what is it, and I couldn't find
> any explanation for that. I appreciate if any of you can give me a short
> description of what is that doing,
>
> Best wishes,
> Hadi
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 18 Sep 2019 18:38:28 +0200
> From: Mahdi Bagherpoor <mehdi.bpour at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] -t option?
> Message-ID:
> <CAM+zo1OzV-p8+j+4YhAhM2eeDbS_=jPGgT9HkT-B=Z8kgWT78w at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Hadi,
>
> It is well explained in Gromacs tutorial, in the below:
> http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html
>
> "Note that we are now including the -t flag to include the checkpoint file
> from the *NVT* equilibration"
>
> Cheers,
> Mahdi
> On Wed, Sep 18, 2019 at 5:43 PM Hadi Rahmaninejad <ha.rahmaani at gmail.com>
> wrote:
>
>> Hello dear users,
>>
>> I am going to run a simulation according to a tutorial, but there is an
>> option of "-t nvt.cpt" that I don't know what is it, and I couldn't find
>> any explanation for that. I appreciate if any of you can give me a short
>> description of what is that doing,
>>
>> Best wishes,
>> Hadi
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 18 Sep 2019 20:36:10 +0000 (UTC)
> From: m g <dr_m_ganj at yahoo.com>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Tetrahedral Order Parameter
> Message-ID: <1547831962.6347867.1568838970913 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Justi,I want to calculate the Tetrahedral Order Parameter (Q) for
> water in my simulation system. I used "gmx hydorder" command but it is not
> clear for me. what kinds of flag must be use exactly? how can I set
> correct number for "-sgang1?and?-sgang2" flags? This command is very
> confusing. how can I get Q?Thanks,Sana
>
> ------------------------------
>
> Message: 6
> Date: Thu, 19 Sep 2019 08:31:30 +1000
> From: Dallas Warren <dallas.warren at monash.edu>
> To: GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Tetrahedral Order Parameter
> Message-ID:
> <CAOv1qzbcbzrxNmqZ1TNf=qvcBpBNFYUdQrgRxeEpz7PJHjOmsA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> I can't provide advice directly, but more generally ... try things out,
> experiment. All it takes is a bit of time and it will help you get a
> better
> understanding of how things work. Plus you will get further faster doing
> it
> yourself, rather than waiting a day or two for someone else to respond
> with
> some help, which may or may not be exactly what you are after. If you
> still
> can't figure it out, post exactly what you have done, what the output was,
> how it deviated from what expected etc.
>
> Plus you should be able to find a few instances of others using the
> command
> via a web search.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Thu, 19 Sep 2019 at 06:36, m g <dr_m_ganj at yahoo.com> wrote:
>
>> Dear Justi,I want to calculate the Tetrahedral Order Parameter (Q) for
>> water in my simulation system. I used "gmx hydorder" command but it is
>> not
>> clear for me. what kinds of flag must be use exactly? how can I set
>> correct
>> number for "-sgang1 and -sgang2" flags? This command is very confusing.
>> how
>> can I get Q?Thanks,Sana
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> --
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>
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> End of gromacs.org_gmx-users Digest, Vol 185, Issue 59
> ******************************************************
>
--
Man Hoang Viet
Institute of Physics,
Polish Academy of Sciences.
Al. Lotnikow 32/46
02-668 Warsaw, Poland.
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