[gmx-users] N-terminus problem

Mon Jul 4 17:34:21 CEST 2011

On 4/07/2011 11:49 PM, Emine Deniz Tekin wrote:
>
> Hi Mark,
>
> Thank you for your reply.
>
> Let me explain the problem a little more and answer your questions. I 
> would be happy if you could expound upon your reply.
>

Sorry, I can't.

* I won't try to make sense of five different font styles and a forest 
of differential indentation.
* You didn't say whether you tested the single lipopeptide topology like 
I suggested. Solve simple problems completely before tackling complex 
problems.
* I pointed out that showing us only the coordinate file was not an 
effective way of diagnosing a mismatch of topology database and 
coordinate file naming, and you still haven't supplied any topology 
information.
* The *geometry* of the lipopetides is often irrelevant for trying to 
get pdb2gmx to construct a *topology*

Mark

>        Hi Gromacs users,
>
>>     I created a lipopeptide (lauroic acid connected to an 8-residue
>>     peptide which starts with Valine). 
>     How is the link from acid to peptide created?
>
>     The link between acid and peptide is a “peptide bond”.
>
>     (I prepared the *rtp *entry for the lauroic acid make a peptide bond as if lauroic acid was an amino acid (following your suggestion)).
>
>
>     If I try to use “pdb2gmx” for ONE LİPOPEPTİDE (9 residues), that is
>
>     pdb2gmx –f one_lipopeptide.pdb -ter
>
>     It seems to work. That is, topol.top is created. (And also this
>     topology works for MD.)
>
>     Does that topology work for MD? Why does pdb2gmx think there's 9
>     residues, and below there seem to be 63?
>
> ·But, if I try to use “pdb2gmx” for SEVEN LİPOPEPTİDE at desired 
> positions (63 residues), that is
>
> pdb2gmx –f seven_lipopeptide.pdb -ter
>
> It gives the fatal error: “Atom N not found in residue seq.nr 
> <http://seq.nr/>. 1 while adding improper”
>
>>     While I was creating the lipopeptide, I introduced the lauroic
>>     acid as a pseudo amino acid (following Mark’s suggestion). So, I
>>     really do NOT have atom N in the first residue. I pasted a part
>>     of my gro file below.
>>
>     Some improper in your topology database entries wants a N atom
>     that doesn't exist. Unfortunately, we don't have anywhere near
>     enough information to guess why. pdb2gmx is trying to match your
>     .rtp and specbond entries to your .gro file, but only seeing the
>     latter can't help diagnose a mismatch. Some description of
>     "desired positions" is also important.
>
>
> I wrote a code to put 7 identical lipopeptides at desired positions. 
> That is, 7 lipopeptides are placed on a plane with 15 degree angle 
> between the adjacent lipopeptides.
>
>
>
>     Also, giving full command lines are always preferred. You may not
>     think anything significant is there, and you might be right, but
>     if there *can* be something significant there, and we aren't given
>     the chance to know whether it is present, we might just not bother
>     to waste time guessing :)
>
>
> I used gromos53a6 force field (extended to include lauroic acid 
> parameters) & spc type water
>
>
> And also, I have a question: The first residue in my pdb file is 
> lauroic acid that is DPP, second residue is Valine and so on.. But 
> when I used the pdb2gmx with –ter it says: Start terminus VAL-2: None, 
> End terminus ASP-9: COO-) Would not DPP residue be the start terminus?
>
> Best regards,
>
> Mark
>
>     Deniz
>>
>>
>>     GROMACS molecule input test
>>
>>     574
>>
>>     1DPPCA111.0275.2953.153
>>
>>     1DPPCB210.8945.2993.078
>>
>>     1DPPCG310.7775.2343.153
>>
>>     1DPPCD410.6455.2543.078
>>
>>     1DPPCE510.5215.2033.153
>>
>>     1DPPCZ610.3925.2513.086
>>
>>     1DPPCM710.2665.2073.161
>>
>>     1DPPCN810.1405.2723.103
>>
>>     1DPPCO910.0145.2213.172
>>
>>     1DPPCP109.8855.2793.112
>>
>>     1DPPCQ119.7615.2033.160
>>
>>     1DPPC1211.1015.4303.147
>>
>>     1DPPO1311.0325.5313.136
>>
>>     2VALN1411.2355.4503.160
>>
>>     2VALH1511.2495.5503.159
>>
>>     2VALCA1611.3685.3853.181
>>
>>     2VALCB1711.3905.2333.181
>>
>>     2VALCG11811.3325.1723.308
>>
>>     2VALCG21911.3385.1613.056
>>
>>     2VALC2011.4865.4493.103
>>
>>     2VALO2111.4985.4362.982
>>
>>     …………..
>>
>>     63ASPOD1570-0.30614.8743.343
>>
>>     63ASPOD2571-0.45115.0303.289
>>
>>     63ASPC572-0.05715.0233.106
>>
>>     63ASPO15730.01415.0033.207
>>
>>     63ASPO2574-0.02915.1043.017
>>
>>     16.2393716.2393716.23937
>>
>>
>>     I am using Gromacs 53a6 force field and gromacs 4.5.3 version.
>>
>>     Any help will be appreciated.
>>
>>     Thanks in advance
>>
>>     Deniz
>>
>
>
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