[gmx-users] topology problem with x2top
paul buscemi
pbuscemi at q.com
Thu Oct 4 16:02:09 CEST 2018
> On Oct 4, 2018, at 8:30 AM, Paul Buscemi <busce004 at umn.edu> wrote:
>
>
>
> Maria
>
> Regarding PVDF ( in 54a7 ff) here is some information that may be useful:
> =========================== Input command to generate a 15 mer ===========
> gb at RGB ~/Desktop/PVDF $ gmx x2top -f pdb/PVDF15.pdb -o pvdf.top -ff select
> :-) GROMACS - gmx x2top, 2018 (-:
>
>
> Command line:
> gmx x2top -f pdb/PVDF15.pdb -o pvdf.top -ff select
>
>
> Select the Force Field:
> From current directory:
> 1: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
> From '/usr/local/gromacs/share/gromacs/top':
> 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
> 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> 4……
…...
> 1
>
> There are 4 different atom types in your sample
> Generating angles and dihedrals from bonds...
> Before cleaning: 279 pairs
> Before cleaning: 279 dihedrals
> There are 31 proper dihedrals, 0 impropers, 192 angles
> 279 pairs, 97 bonds and 98 atoms
> Total charge is -0.0759998, total mass is 990.64
>
>
>
> ========================== part of the itp from ATB used to obtain charges and types from a 3-mer ========
>
> [ moleculetype ]
> ; Name nrexcl
> 37YP 3
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass total_charge
> 1 HC 1 37YP H26 1 0.155 1.0080
> 2 C 1 37YP C23 1 -0.493 12.0110
> 3 HC 1 37YP H24 1 0.155 1.0080
> 4 HC 1 37YP H25 1 0.155 1.0080
> 5 C 1 37YP C20 1 0.530 12.0110
> 6 F 1 37YP F21 1 -0.237 18.9984
> 7 F 1 37YP F22 1 -0.237 18.9984
> 8 C 1 37YP C17 1 -0.410 12.0110
> 9 HC 1 37YP H18 1 0.157 1.0080
> 10 HC 1 37YP H19 1 0.157 1.0080 ; -0.068
> 11 C 1 37YP C14 2 0.627 12.0110
> 12 F 1 37YP F15 2 -0.236 18.9984
> 13 F 1 37YP F16 2 -0.236 18.9984
> 14 C 1 37YP C11 2 -0.494 12.0110
> 15 HC 1 37YP H12 2 0.159 1.0080
> 16 HC 1 37YP H13 2 0.159 1.0080
> 17 C 1 37YP C8 2 0.475 12.0110
> 18 F 1 37YP F9 2 -0.227 18.9984
> 19 F 1 37YP F10 2 -0.227 18.9984 ; 0.000
> 20 C 1 37YP C5 3 0.017 12.0110
> 21 HC 1 37YP H6 3 0.044 1.0080
> 22 HC 1 37YP H7 3 0.044 1.0080
> 23 C 1 37YP C2 3 -0.280 12.0110
> 24 HC 1 37YP H1 3 0.081 1.0080
> 25 HC 1 37YP H3 3 0.081 1.0080
> 26 HC 1 37YP H4 3 0.081 1.0080 ; 0.06
>
>
> ==== below -the n2t used for several polymers - added to the Gtomod54a7 directory =========
=================== last two lines for PVDF =====================
================= no guarantee at all that charges are correct/optimal/best or even good ====
>
>
>
> ; atom type charge mass
> H HC .019 1.008 1 C 0.108
> C C -.053 12.035 4 C .154 H 0.108 H 0.108 H 0.108 ; methyl
> C CH2 -0.0506 12.011 4 H 0.108 H 0.108 C 0.152 C 0.152 ; ethyl
>
> C C .302 12.0011 4 C .152 N .144 H .108 H .108 ; amide
> N NT -.387 14.0067 3 C .139 C .1537 H .0985 ;C-NH-C
> C C .021 12.011 3 C .153 N .139 O .1207
> C c .021 12.001 3 O .127 O .122 N .138
>
> N NT -.027 14.0067 3 C .139 HS14 .0985 HS14 .0985 ; C-NH2
> C C .021 12.011 4 C .153 C .153 N .139 H .113
> C C -.021 12.011 4 C .153 O .139 H .109 H .108 ; ether
>
> O O -.371 15.999 1 C .1207 ; O=C acid
> O OE -.287 15.999 2 C .1204 C .1204 ; ether
> H HS14 .0528 1.008 1 N .0985 ; N-H
>
> F F -.214 18.9984 1 C .1386
> C C 0.435 12.011 4 F .1385 F .1385 C .1548 C .1548
>
> ============ outcome -============
> grommp complains about 0.07 charge, but with maxwarn produces the em and nvt files.
It is up to you to decide if this is acceptable.
Check that you ave atom types for the terminal atoms. it they are incorrect it throws off all else.
Also, somehing I often miss. bond lengths in nm, not angstroms
You might try using 54a7 in a test run - that may pinpoint your error in oplass
Using this method, I’ve made up to a 500 mer without much head scratching.
hope this helps ,
Paul
> On Oct 4, 2018, at 2:45 AM, Maria Luisa <ml.perrotta at itm.cnr.it> wrote:
>
> Dear Dallas the command are:
> FOR PVDF
> gmx x2top -f PVDF_chain.gro -o PVDF_chain.top -ff oplsaa -name
>
> the system gives me this lines:
>
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t
>
> There are 23 names to type translations in file oplsaa.ff
>
> Generating bonds from distances...
>
> atom 44
>
> Can not find forcefield for atom C21-2 with 3 bonds
>
> Can not find forcefield for atom C18-5 with 3 bonds
>
> Can not find forcefield for atom C16-10 with 3 bonds
>
> etc etc
> Fatal error:
>
> Could only find a forcefield type for 302 out of 602 atoms
>
> The same thing happens with graphene oxide. The problem is that I built in
> the past combined systems of these two molecules, without problems. I
> created an executable n2t file as I mentioned in the previous post.
>
> Maria Luisa
> Thank you for your help
>
>
>> Sorry, can't help you directly, but can you post some of the commands
>> that you've actually run (copy and paste the exact lines), then the
>> error messages that you get (again a direct copy and past). Be as
>> specific as you can be, including the different things you have
>> attempted to use, and the results.
>>
>> The more exact details you give, the more able people are to help.
>>
>> 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 Wed, 3 Oct 2018 at 19:32, Maria Luisa <ml.perrotta at itm.cnr.it> wrote:
>>>
>>> Dear users,
>>> I need help. I want to build the topology of a polymeric chain of PVDF
>>> of
>>> 602 atoms, and of a sheet of Graphene Oxide of 202 atoms. I use the
>>> version of gromacs 5.1.4. The problem is that it does not recognize some
>>> atoms in the polymeric chain, and not at all the graphene oxide atoms. I
>>> already worked with the x2top command, I had already created another
>>> executable .n2t file, to complete the missing atoms in the atomname
>>> file,
>>> and in the past I built topology for graphene oxide and graphene
>>> systems,
>>> but now, all this command with my previous challenge doesn't t work. I'm
>>> doing a thousand tests but I do not know how to do it.
>>>
>>> I hope to get help.
>>> Thank you
>>>
>>> Maria Luisa Perrotta
>>> Ph.D Student, CNR-ITM
>>> via P.Bucci, 87036 Rende (Cs)
>>> Italy
>>> email: ml.perrotta at itm.cnr.it
>>>
>>>
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>
>
> Maria Luisa Perrotta
> Ph.D Student, CNR-ITM
> via P.Bucci, 87036 Rende (Cs)
> Italy
> email: ml.perrotta at itm.cnr.it
>
>
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