[gmx-users] error in grompp command

Thu Jul 3 12:27:38 CEST 2014

hello gromacs users now have been removed this error after changing the
number of SOL in topol_popc.top file (counted from popc128.gro)
after that i hav used -maxwarn 1 command

result is

Generated 813 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'
Warning: atom name 6657 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6658 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6659 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6660 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6661 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6662 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6663 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6664 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6665 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6666 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6667 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6668 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6669 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6670 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6671 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6672 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6673 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6674 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6675 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6676 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
(more than 20 non-matching atom names)

WARNING 1 [file topolpopc.top, line 26]:
  7380 non-matching atom names
  atom names from topolpopc.top will be used
  atom names from popc128.gro will be ignored

Analysing residue names:
There are:   128      Other residues
There are:  2460      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group rest is 34725.00
Largest charge group radii for Van der Waals: 0.216, 0.216 nm
Largest charge group radii for Coulomb:       0.216, 0.216 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 54x54x60, spacing 0.116 0.114 0.115
Estimate for the relative computational load of the PME mesh part: 0.36
This run will generate roughly 164 Mb of data

There was 1 warning

how tom resolve these problems
em.tpr is formed but rest of the files are not formed
help

On Thu, Jul 3, 2014 at 2:23 PM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> hello everyone
> my grompp related   problem atomtype CA not found has been solved now i am
> using 56a3 force field for protein ligand complex with popc but srill i
> didnt get em.tpr a new error
>
>
>
> Excluding 3 bonded neighbours molecule type 'POPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line:
> 523
>
> Fatal error:
> number of coordinates in coordinate file (popc128.gro, 14036)
>              does not match topology (topolpopc.top, 17459)
> kindly help
>
>
>
> On Wed, Jul 2, 2014 at 3:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/2/14, 6:07 AM, RINU KHATTRI wrote:
>>
>>> hello gromacs users
>>>   i used 43a1 force field(Gromacs 4.5.7) in the atomtype.atp file in the
>>> place of CA CA2+ is present in ffnonbonded.itp file CA and CA2+ both are
>>> present according to tutorial i have been followed  all the step
>>> still em.tpr not formed
>>> atomtype CA not found
>>>
>>>
>> "CA" is the gmx.ff nomenclature for the calcium type, so that suggests
>> you're mixing and matching force fields (note that gmx.ff has been removed
>> from the latest Gromacs version, since it should not be used).  Without
>> explicit detail of your topology (i.e. post your files so they can be
>> downloaded), there's very little that can be done to suggest where things
>> have gone wrong.  I strongly suspect you've mixed and matched force fields
>> somewhere, which is easy to do when dealing with complex systems.  Pick a
>> force field, stick to it exactly.
>>
>> -Justin
>>
>>
>>
>>> On Wed, Jul 2, 2014 at 3:19 PM, ERASTOVA V. <
>>> valentina.erastova at durham.ac.uk
>>>
>>>> wrote:
>>>>
>>>
>>>  Hi Rinu,
>>>>
>>>> See what forcefield files you include in your topology, then go to the
>>>> force field folders and check if those indeed have that atom types.
>>>> You must indeed be missing the CA type. Likely, you just forgot to
>>>> include
>>>> some topology file.
>>>>
>>>> V
>>>>
>>>>
>>>>
>>>>
>>>> On 2 Jul 2014, at 10:23, gromacs.org_gmx-users-request@
>>>> maillist.sys.kth.se
>>>> <mailto:gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 2
>>>> Date: Wed, 2 Jul 2014 12:26:07 +0530
>>>> From: RINU KHATTRI <nickname.mittu at gmail.com<mailto:
>>>> nickname.mittu at gmail.com>>
>>>> To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
>>>> Subject: [gmx-users] error in grompp command
>>>> Message-ID:
>>>> <CAOEfx3KBphAK_BRP4L4orCp_gSBsuSOHNLUgHX0WyJweWuaN9A at mail.gmail.com
>>>> <mailto:CAOEfx3KBphAK_BRP4L4orCp_gSBsuSOHNLUgHX0WyJweWuaN9A@
>>>> mail.gmail.com
>>>>
>>>>>
>>>>>>  Content-Type: text/plain; charset=UTF-8
>>>>
>>>> hello gromacs
>>>> i an working on protein ligand complex with lipid membrane (popc)
>>>>
>>>> grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn
>>>> -1
>>>>
>>>> after this fatal error atomtypes CA not found
>>>> and only md.oonly mdout is formed
>>>> kindly help
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> --
>>>> Gromacs Users mailing list
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>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
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>
>