[gmx-users] error in grompp command

[Justin Lemkul]

On 7/3/14, 6:27 AM, RINU KHATTRI wrote:
> 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

In this case, the warnings about non-matching names are harmless and they refer 
only to different conventions in water nomenclature.  You can easily re-name the 
atoms in the coordinate file with simple sed statements, but it's not necessary 
here.  Ignoring mismatching names in other cases can be very harmful, so be advised.

> em.tpr is formed but rest of the files are not formed

What other files are you looking for?  The purpose of grompp is to produce a 
.tpr file; there are other files that can be produced, but none of them are 
essential.

-Justin

-- 
==================================================

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

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