[gmx-users] if PRODRG calculate incorrectly
ahmet yıldırım
ahmedo047 at gmail.com
Sat Sep 17 15:28:19 CEST 2011
Dear Tsjerk and Justin,
Thanks for your reply. I will contact the PRODRG developers.
can you suggest anyway/anytool for generating ligand coordinates/topologies?
Thanks in advance
17 Eylül 2011 15:58 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:
>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>> I have a problem related to PRODRG.
>>
>> Chirality:NO
>> Full charges: YES
>> Energy minimization: NO
>>
>> _*İnput file name:TRS.pdb*_
>> HETATM 1803 C TRS B 232 38.588 -4.733 65.956 1.00 17.99
>> C ANISOU 1803 C TRS B 232 2126 1948 2760 -378 45 -81
>> C HETATM 1804 C1 TRS B 232 40.103 -5.057 65.899 1.00 16.81
>> C ANISOU 1804 C1 TRS B 232 1642 1577 3168 -531 171
>> 120 C HETATM 1805 C2 TRS B 232 37.795 -5.994 66.343 1.00
>> 20.76 C ANISOU 1805 C2 TRS B 232 2790 2021 3077 67
>> 141 -408 C HETATM 1806 C3 TRS B 232 38.160 -3.717 67.031
>> 1.00 16.86 C ANISOU 1806 C3 TRS B 232 2240 1557 2611
>> -491 8 -192 C HETATM 1807 N TRS B 232 38.227 -4.154
>> 64.652 1.00 18.26 N ANISOU 1807 N TRS B 232 2336 2520
>> 2083 -166 46 -112 N HETATM 1808 O1 TRS B 232 40.741
>> -4.020 65.158 1.00 17.53 O ANISOU 1808 O1 TRS B 232 1921
>> 1579 3163 -225 147 197 O HETATM 1809 O2 TRS B 232
>> 37.871 -6.803 65.211 1.00 23.91 O ANISOU 1809 O2 TRS B 232
>> 3018 2456 3610 -48 -86 -450 O HETATM 1810 O3 TRS B 232
>> 38.871 -2.531 66.874 1.00 18.28 O ANISOU 1810 O3 TRS B
>> 232 2677 1594 2673 197 -4 -52 O
>>
>> I get the output _as the following file1.itp_ from your PRODRG server for
>> TRS ligand before 3-4 months. I think this calculate is correct:
>> *_file1.itp_*
>> ................
>> [ moleculetype ]
>> ; Name nrexcl
>> TRS 3
>>
>> [ atoms ]
>> ; nr type resnr resid atom cgnr charge mass
>> 1 OA 1 TRS O1 1 -0.240 15.9994 2
>> H 1 TRS HAA 1 0.052 1.0080 3 CH2 1 TRS
>> C1 1 0.061 14.0270 4 CH1 1 TRS C 1
>> 0.127 12.0110 5 CH2 1 TRS C3 2 0.090 14.0270
>> 6 OA 1 TRS O3 2 -0.165 15.9994 7
>> H 1 TRS HAC 2 0.075 1.0080 8 NL 1 TRS
>> N 3 0.876 14.0067 9 H 1 TRS HAE 3
>> 0.041 1.0080 10 H 1 TRS HAF 3 0.042 1.0080
>> 11 H 1 TRS HAD 3 0.041 1.0080 12
>> CH2 1 TRS C2 4 0.090 14.0270 13 OA 1 TRS
>> O2 4 -0.165 15.9994 14 H 1 TRS HAB 4
>> 0.075 1.0080 ....................
>>
>>
>> But Now, That is, today, I get the output _as the following file2.itp_
>> from your PRODRG server for TRS ligand.
>> *_file2.itp_*
>> .....
>> [ moleculetype ]
>> ; Name nrexcl
>> TRS 3
>>
>> [ atoms ]
>> ; nr type resnr resid atom cgnr charge mass
>> 1 OA 1 TRS O1 1 -0.173 15.9994 2
>> H 1 TRS H13 1 0.061 1.0080 3 CH2 1 TRS
>> C1 1 0.165 14.0270 4 CCL4 1 TRS C 1
>> 0.177 12.0110 5 CH2 1 TRS C3 1 0.165 14.0270
>> 6 OA 1 TRS O3 1 -0.174 15.9994 7
>> H 1 TRS H33 1 0.062 1.0080 8 NL 1 TRS
>> N 1 0.675 14.0067 9 H 1 TRS H2 1
>> 0.014 1.0080 10 H 1 TRS H3 1 0.014 1.0080
>> 11 H 1 TRS H1 1 0.014 1.0080 12
>> CH2 1 TRS C2 2 0.144 14.0270 13 OA 1 TRS
>> O2 2 -0.198 15.9994 14 H 1 TRS H23 2
>> 0.054 1.0080 ....
>>
>> Now, I think PRODRG calculate incorrectly cgnr charge
>>
>>
> I agree with Tsjerk that you should contact the PRODRG developers regarding
> the differences, but I would also say that neither of these files is
> correct. PRODRG has never given reliable charges. See, for instance
> (something I posted dozens of times before):
>
> http://pubs.acs.org/doi/abs/**10.1021/ci100335w<http://pubs.acs.org/doi/abs/10.1021/ci100335w>
>
> -Justin
>
>
> What should I do? can you help me?
>>
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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--
Ahmet YILDIRIM
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