On 10/6/12 1:27 PM, Shima Arasteh wrote:
Dear Justin,
I downloaded popc.pdb file from
http://terpconnect.umd.edu/~jbklauda/research/download.html. This pdb file has
water molecules. So I tried to run these commands and don't run genbox:
1.editconf -f popc.pdb -o popc.gro -c -d 1.0 -bt cubic
If you have a pre-equilibrated membrane, complete with water, this doesn't make
sense. You're introducing empty space around the whole system.
2.grompp -f em.mdp -c popc.gro -p topol.top -o em.tpr
I also added the SOL molecules manually as it is written at the end of the
popc.pdb file downloaded.
I don't understand why you need to do this.
But this fatal errors comes out:
Generated 21528 of the 21528 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 18355 of the 21528 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'
Warning: atom name 2 in topol.top and popc.gro does not match (C12 - C11)
Warning: atom name 3 in topol.top and popc.gro does not match (C13 - C12)
Warning: atom name 4 in topol.top and popc.gro does not match (C14 - C13)
Warning: atom name 5 in topol.top and popc.gro does not match (C15 - C14)
Warning: atom name 6 in topol.top and popc.gro does not match (H12A - H11)
Warning: atom name 7 in topol.top and popc.gro does not match (H12B - H12)
Warning: atom name 8 in topol.top and popc.gro does not match (H13A - H21)
Warning: atom name 9 in topol.top and popc.gro does not match (H13B - H22)
Warning: atom name 10 in topol.top and popc.gro does not match (H13C - H23)
Warning: atom name 11 in topol.top and popc.gro does not match (H14A - H31)
Warning: atom name 12 in topol.top and popc.gro does not match (H14B - H32)
Warning: atom name 13 in topol.top and popc.gro does not match (H14C - H33)
Warning: atom name 14 in topol.top and popc.gro does not match (H15A - H41)
Warning: atom name 15 in topol.top and popc.gro does not match (H15B - H42)
Warning: atom name 16 in topol.top and popc.gro does not match (H15C - H43)
Warning: atom name 17 in topol.top and popc.gro does not match (C11 - C15)
Warning: atom name 18 in topol.top and popc.gro does not match (H11A - H51)
Warning: atom name 19 in topol.top and popc.gro does not match (H11B - H52)
Warning: atom name 20 in topol.top and popc.gro does not match (P - P1)
Warning: atom name 21 in topol.top and popc.gro does not match (O13 - O3)
(more than 20 non-matching atom names)
WARNING 1 [file topol.top, line 36]:
8382 non-matching atom names
atom names from topol.top will be used
atom names from popc.gro will be ignored
These warnings suggest that the coordinate file is out of sync with respect to
the atoms in the topology. Bad things will happen, because the wrong parameters
are mapped to the wrong atoms.
-Justin
Analysing residue names:
There are: 72 Other residues
There are: 2242 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 42393.00
Largest charge group radii for Van der Waals: 0.040, 0.040 nm
Largest charge group radii for Coulomb: 0.079, 0.079 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 96x96x96, spacing 0.116 0.116 0.116
Estimate for the relative computational load of the PME mesh part: 0.59
NOTE 1 [file em.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing
This run will generate roughly 191 Mb of data
There was 1 note
There was 1 warning
-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file:
/home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/grompp.c, line: 1584
Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
Would you please give me advice? Thanks for all your explanation.
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <[email protected]>
To: Shima Arasteh <[email protected]>
Cc: Discussion list for GROMACS users <[email protected]>
Sent: Saturday, October 6, 2012 7:25 PM
Subject: Re: [gmx-users] Model of water
On 10/6/12 11:52 AM, Shima Arasteh wrote:
The total atom of popc-solv.gro is 74672
grep HW gives me 48698
Assuming you meant to type 48696 like you reported before, this means there are
24348 water molecules, since there are two HW atoms per water (HW1 and HW2). If
you grep for OW (since it is unique to each water molecule), you can confirm the
count.
grep P gives me 1628
I already said this grep was insufficiently precise and thus it is not possible
to connect this information with the topology.
Section of moleculetypes in top file is as
[ molecules ]
Compound #mols
POPC 238
SOL 24348
I am confused! Am I need to change the number of gro or top file? Actually I
can't make connection between gro and top, so the coordinate doesn't match
topology yet!!
You need to make the topology agree with the coordinate file. Do not make
manual adjustments to the .gro file. Sometimes it's better to start over and be
more careful. A mismatch between coordinates and topology always boils down to
errors in bookkeeping.
-Justin
Please help me :(
Sincerely,
Shima
----- Original Message -----
From: Shima Arasteh <[email protected]>
To: Justin Lemkul <[email protected]>; Discussion list for GROMACS users
<[email protected]>
Cc:
Sent: Saturday, October 6, 2012 6:22 PM
Subject: Re: [gmx-users] Model of water
# grep -c P popc-solv.gro
1628
What should I do with this number?
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <[email protected]>
To: Shima Arasteh <[email protected]>
Cc:
Sent: Saturday, October 6, 2012 6:17 PM
Subject: Re: [gmx-users] Model of water
On 10/6/12 10:45 AM, Shima Arasteh wrote:
Yes, the system is only POPC and water.
Then it should be very easy to count how many molecules are in the system using
grep. Your topology specifies a lot more atoms than the coordinate file has.
The number of water molecules appears right, which leaves only the number of
POPC as the problem.
-Justin
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <[email protected]>
To: Shima Arasteh <[email protected]>
Cc:
Sent: Saturday, October 6, 2012 6:07 PM
Subject: Re: [gmx-users] Model of water
On 10/6/12 10:32 AM, Shima Arasteh wrote:
OK.
I did as follow as I described, but there is an error:
1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic
2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top
Then added #include "charmm36.ff/tip3p.itp" to topol.top
3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr
Fatal error:
number of coordinates in coordinate file (popc-solv.gro, 74672)
does not match topology (topol.top, 104936)
I checked the water molecules of popc-solv.gro by grep command ;
# grep -c HW popc-solv.gro
48696
[ molecules ]
; Compound #mols
POPC 238
SOL 24348
What is the problem? would you please help me? I think the SOL molecule are
counted twice!!
You're off by a huge amount of atoms, so something is very wrong. The water
molecules do not appear to be the problem. The number of HW/2 is equal to the
number of SOL molecules. Is the system only POPC in water? No protein or any
other components?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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