[gmx-users] Diagnosing + system blowing up
shima_arasteh2001 at yahoo.com
Sun Jul 29 13:09:37 CEST 2012
Thanks dear Mark.
I don't use ignh. This is the command of pdb2gmx which I enter:
pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter
grompp does not give me the warning of that the atom names in the topology and the coordinate file don't match, instead it gives me that there are no default bonds/dihedrals ( Now I can see atom 18 in all lines which is defined by grompp)
So, change this line of .hdb
1 1 H1 C N O
1 1 H1 CN N ON
N is the N of Valine and ON is the O of formyl.
I'll check it out right now.
----- Original Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, July 29, 2012 2:48 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
On 29/07/2012 7:55 PM, Shima Arasteh wrote:
> I listened to you absolutely and didn't proceed any other way! What I created in .rtp file for FVAL ( like what you described sometime ago), is as below:
> First of all added the FVAL to residuetyes.dat.
> Then added to .rtp file:
> [ FVAL ]
> [ atoms ]
> CN C 0.357 0
> ON O -0.51 1
> H1 HA 0.100 2
> N NH1 -0.423 3
> HN H 0.333 4
> CA CT1 0.034 5
> HA HB 0.09 6
> CB CT1 -0.093 7
> HB HA 0.09 8
> CG1 CT3 -0.268 9
> HG11 HA 0.09 10
> HG12 HA 0.09 11
> HG13 HA 0.09 12
> CG2 CT3 -0.268 13
> HG21 HA 0.09 14
> HG22 HA 0.09 15
> HG23 HA 0.09 16
> C C 0.528 17
> O O -0.510 18
> [ bonds ]
> CN H1
> CN ON
> CN N
> N H
You don't have an atom named H, but maybe this is succeeding because I
patched pdb2gmx to accept HN or H in some cases...
> CA N
> CA HA
> CA C
> C O
> CA CB
> CB HB
> CB CG1
> CB CG2
> CG2 HG21
> CG2 HG22
> CG2 HG23
> CG1 HG11
> CG1 HG12
> CG1 HG13
> [ impropers ]
> CN N ON H1
> And at last adding H atoms to .hdb:
> 1 1 H1 C N O
Why are you adding your formyl hydrogen to the carbon named C, which is
part of the peptide bond after valine? Here's your problem. You're
presumably using pdb2gmx -ignh (but you should be copying your pdb2gmx
command into your email so we're not wasting time guessing...) H is
being added back in as atom 1, and so you have a bond from the new atom
1 to atom 18 (that carbon). Probably, that's being matched to the
coordinates of the original CN atom (leading to the long bond warning,
and then to blowing up), grompp is warning you that the atom names in
the topology and the coordinate file don't match, and you've been
ignoring that warning too. There's a reason all the
http://www.gromacs.org/Support page asks for copied and pasted input and
output, evidence of modified files, and for you to have read all the
output. I suspect there's been a lot of time wasted on this thread ;-)
> 1 1 HN N C CA
> 1 5 HA CA N C CB
> 1 5 HB CB CA CG1 CG2
> 3 4 HG1 CG1 CB CA
> 3 4 HG2 CG2 CB CA
> I tried to follow your suggestion exactly! Believe me! :-)
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Sunday, July 29, 2012 1:14 AM
> Subject: Re: [gmx-users] Diagnosing + system blowing up
> On 7/28/12 2:47 PM, Shima Arasteh wrote:
>> Dear Mark, Thanks for your suggestions.
>> Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all! However I see this pair in the [pairs] section of topology !
>> So I can get the result of an inappropriate bond interaction here! Correct?
>> Now I think it's not necessary to go through the diagnosing steps any more! :-(
>> What is my duty right now?!
>> Is this problem supposed to be fixed in the .pdb file? What's wrong with the pdb file? What about erasing the unexpected bond interactions in topology file?
> You'll need to back up and provide more information here. I recall our discussion several weeks ago about this formylated valine problem, which was solved by creating a special residue called FVAL. If you created a correct .rtp entry like I described, this shouldn't be happening.
> If you're proceeded some other way, you will have to specify exactly what you've done up to this point. This may require snippets of relevant residues in coordinate files, .rtp entries, etc. Without this information, everything I've seen thus far is a jumbled mess that is nearly impossible for anyone on this list to troubleshoot.
> -- ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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