[gmx-users] number of coordinates does not match after POSRES
Simon Kit Sang Chu
simoncks1994 at gmail.com
Thu Jun 8 06:24:15 CEST 2017
Hi Justin,
Thanks for your advice. Since we are using a forcefield which could only
incorporate with gromacs 3.3.1, we have no choice but to prepare the system
in the old version, then run it with the latest version of gromacs.
Yes, indeed the option should be with -DPOSRES instead. And the topology
file should #include chainA-pace.top, then chainA_posres.itp in this
alternative manner. It seems that writing all chainA chainB.top first and
all pores.itp later would not do it. Please tell me if I am wrong.
Simon
2017-06-07 19:57 GMT+08:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 6/7/17 7:18 AM, Simon Kit Sang Chu wrote:
>
>> Hi Mark,
>>
>> Thanks for your prompt reply. What surprises me is that a change of
>> "define
>> = POSRES" could cause a problem. The full output from grompp is -
>>
>> checking input for internal consistency...
>> calling cpp...
>> cpp: error: POSRES: No such file or directory
>>
>
> Well, here's the first problem. Your syntax is incorrect (#ifdef keywords
> are prefixed with -D, so "define = POSRES" does nothing but "define =
> -DPOSRES" would invoke position restraints.
>
> cpp: warning: ‘-x c’ after last input file has no effect
>> cpp: fatal error: no input files
>> compilation terminated.
>> cpp exit code: 1024
>> Tried to execute: 'cpp -I/home/simon/Softs/gromacs-3.
>> 3.1/share/gromacs/top
>> POSRES p1p2.top > gromppDTyNuM'
>> The 'cpp' command is defined in the .mdp file
>> processing topology...
>> processing coordinates...
>> -------------------------------------------------------
>> Program grompp, VERSION 3.3.1
>>
>
> Is there a reason you are using prehistoric, deprecated software?
>
> Source code file: grompp.c, line: 448
>>
>> Fatal error:
>> number of coordinates in coordinate file (npt.gro, 74787)
>> does not match topology (p1p2.top, 0)
>>
>>
> This suggests mangled syntax, so check for typos, bad line endings, etc.
> and use a more modern GROMACS version.
>
> -Justin
>
>
>> The additional information is attached here as a reference.
>>
>> *chainA-pace.top*
>> [ moleculetype ]
>> ; Name nrexcl
>> Protein_A 3
>>
>> [ atoms ]
>> ; nr type resnr residue atom cgnr charge mass typeB
>> chargeB massB
>> 1 N+ 1 MET N 1 0.7 17 ;
>> qtot 0.7
>> .
>> .
>> .
>> 919 922 921 920 2 0.0 300.0
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "chainA_posre.itp"
>> #endif
>>
>>
>> *chainA_porse.itp*
>>
>> ; position restraints for r_1-62_&_Backbone of FullP1P2 in water
>>
>> [ position_restraints ]
>> ; i funct fcx fcy fcz
>> 1 1 1000 1000 1000
>> .
>> .
>> .
>> 523 1 1000 1000 1000
>> 530 1 1000 1000 1000
>>
>> Simon
>>
>>
>> 2017-06-07 16:28 GMT+08:00 Mark Abraham <mark.j.abraham at gmail.com>:
>>
>> Hi,
>>>
>>> We can't tell, because position restraints are an attribute of
>>> moleculetypes and those are hidden in your itp files and you didn't share
>>> which moleculetype grompp reported was the problem. Please copy and paste
>>> terminal output to make a useful description.
>>>
>>> You'll need to include the position restraint file appropriate to each
>>> moleculetype, of course - not the same one each time.
>>>
>>> Mark
>>>
>>> On Wed, 7 Jun 2017 08:58 Simon Kit Sang Chu <simoncks1994 at gmail.com>
>>> wrote:
>>>
>>> Hi,
>>>>
>>>> Initially, my topology file can run grompp with .mdp and .gro. However,
>>>> after putting POSRES in my mdp, the warning "number of coordinates does
>>>>
>>> not
>>>
>>>> match" and there is no coordinate recognized in my topology file
>>>> anymore.
>>>> Therefore, the option POSRES somehow changes everything.
>>>>
>>>> The topology file is put here. Is there anything I have written
>>>> incorrectly?
>>>>
>>>> ; Include forcefield parameters
>>>> #include "ffPACE_1.3.itp"
>>>>
>>>> ; Include chain topologies
>>>> #include "chainA-pace.top"
>>>> #include "chainB-pace.top"
>>>>
>>>> ; Include water topology
>>>> #include "cgWater.itp"
>>>>
>>>> ; Include topology for ions
>>>> #include "martini_v2.0_ions.itp"
>>>>
>>>> [ system ]
>>>> ; Name
>>>> FullP1P2 in water
>>>>
>>>> [ molecules ]
>>>> ; Compound #mols
>>>> Protein_A 1
>>>> Protein_B 1`
>>>> SOL 72899
>>>> NA+ 20
>>>> --
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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 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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