[gmx-users] grompp does not find atomtype
Dawid das
addiw7 at googlemail.com
Wed Jul 2 10:40:10 CEST 2014
I have managed to deal with this problem in following way:
In topology file some bonding parameters were actually missing but some
bonding parameters were not needed, e.g. U-B or dihedral parameters for
atoms which are not connected, that is they belong to different parts of my
new residue.
I found parameters for the missing ones and hashed (;) them out. Is it what
I can do? Like I say, theses bonding parameters that I hashed out were for
atom types which are not connected directly.
Then I performed minimization with steepest descent and in output file I
got:
4655e+05 Fmax= 6.53501e+03, atom= 1003^MStep= 426, Dmax= 2.5e-06 nm,
Epot= -4.54655e+05 Fmax= 9.45125e+03, atom= 1003^MStep= 427, Dmax= 1.2e-06
nm, Epot= -4.54655e+05 Fmax= 1.25724e+04, atom= 1003^M
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 428 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -4.5465475e+05
Maximum force = 1.7057922e+04 on atom 1003
Norm of force = 1.1677969e+02
But I continued with NVT MD simulation. This is my nvt-md.mdp file:
title = NVT MD
integrator = md
constraints = all-bonds
dt = 0.001
nsteps = 20000
nstenergy = 100
nstlist = 10
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 100
nstxtcout = 1000
xtcprecision = 500
ns_type = grid
coulombtype = PME
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
tcoupl = nose-hoover
tc-grps = Protein SOL NA
tau_t = 0.1 0.1 0.1 ;(3 numbers -> because 3 tc-grps)
ref_t = 100 100 100 ;(3 numbers -> because 3 tc-grps)
Pcoupl = No
gen_vel = yes
gen_temp = 100
gen_seed = 173529
energygrps = Protein SOL NA
constraint_algorithm = LINCS
pbc = xyz
And in my NVT output I got error for LINCS:
relative constraint deviation after LINCS:
rms 0.036755, max 1.509884 (between atoms 998 and 1000)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1001 1003 62.1 0.1410 0.2032 0.1410
1001 1002 68.1 0.1240 0.1962 0.1240
1000 1001 88.1 0.1460 0.3276 0.1460
998 1000 90.0 0.1390 0.3489 0.1390
986 1000 90.7 0.1400 0.2237 0.1400
985 986 30.7 0.1300 0.1499 0.1300
Wrote pdb files with previous and current coordinates
These atoms are those for my new residue. For next step I get more
constraint deviation.
Now, is it possible that this is because of wrong parameters? Or maybe I
should minimize my system further?
Here are all the files:
http://www.speedyshare.com/jjvgd/md-simul.tar.bz2
Thank you in advance for help.
Dawid Grabarek
2014-07-01 0:13 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 6/30/14, 2:23 PM, Dawid das wrote:
>
>> O'right, I have solved this last problem for a new system.
>> Here's a link to all the files:
>>
>> http://www.speedyshare.com/EEXq4/ff-trouble.tar.gz
>>
>> Thank you for your help!
>>
>>
>> 2014-06-30 18:13 GMT+02:00 Dawid das <addiw7 at googlemail.com>:
>>
>> O'right, firstly I have tried to do all the calculations once again for
>>> my
>>> complete protein system and I got the same error but also something more:
>>>
>>> ERROR 1 [file mCherry7.top, line 18152]:
>>> No default U-B types
>>> ERROR 2 [file mCherry7.top, line 18153]:
>>> No default U-B types
>>> ERROR 3 [file mCherry7.top, line 18155]:
>>> No default U-B types
>>> ERROR 4 [file mCherry7.top, line 18157]:
>>> No default U-B types
>>> ERROR 5 [file mCherry7.top, line 18158]:
>>> No default U-B types
>>> ERROR 6 [file mCherry7.top, line 18162]:
>>> No default U-B types
>>> ERROR 7 [file mCherry7.top, line 18172]:
>>> No default U-B types
>>> ERROR 8 [file mCherry7.top, line 18173]:
>>> No default U-B types
>>> ERROR 9 [file mCherry7.top, line 18174]:
>>> No default U-B types
>>> ERROR 10 [file mCherry7.top, line 18175]:
>>> No default U-B types
>>> ERROR 11 [file mCherry7.top, line 18176]:
>>> No default U-B types
>>> ERROR 12 [file mCherry7.top, line 18180]:
>>> No default U-B types
>>>
>>>
>>> Fatal error:
>>> Incorrect number of parameters - found 2, expected 4 or 4 for U-B.
>>>
>>>
> This is the only error I can reproduce with the files you posted. It
> comes directly from the .top file, where you have parameters manually
> defined. They are defined incorrectly for U-B type angles.
>
> 25 24 26 5 108.4 148.532
> 25 24 27 5 108.4 148.532
> 25 24 28 5 111.3 192.882
> 26 24 27 5 108.4 148.532
> 26 24 28 5 111.3 192.882
> ...
> etc.
>
>
> And for my new system, consisting of my new residue and two others at the
>>> N and C end I got following error:
>>>
>>> Fatal error:
>>> Unknown bond_atomtype MH1
>>>
>>>
> I can't reproduce this or the first error. Please be sure to focus
> questions only on what can be reproduced by the files you are providing.
> There's no point trying to troubleshoot multiple things based on unknown
> modifications that you've made.
>
>
> -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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