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tanzouqing

гæ (СÓÐÃûÆø)

[ÇóÖú] VMDÖÐÈçºÎ½«Á½¸öpdbÎļþºÏ³ÉÒ»¸öеÄpdbÎļþ?

VMDÖÐÈçºÎ½«Á½¸öpdbÎļþºÏ³ÉÒ»¸öеÄpdbÎļþ?
ÀýÈç:
Èôtemp-1.pdbºÍtemp-2.pdb,ÎÒÏë°ÑÕâÁ½¸öÎļþºÏ³Étemp.pdbÎļþ,ÊÖ¶¯ºÍconsoleÃüÁîÁ÷ÈçºÎ²Ù×÷?лл
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jiaoyixiong

ÈÙÓþ°æÖ÷ (Ö°Òµ×÷¼Ò)

¡¾´ð°¸¡¿Ó¦Öú»ØÌû

¡ï ¡ï
zh1987hs: ½ð±Ò+2, лл 2012-08-29 15:26:44
Äã°Ñ¡°mol new temp-1.pdb ;mol addfile temp-1.psf¡±
¸Ä³É¡°mol load psf  temp-1.psf pdb temp-1.pdb¡±
8Â¥2012-08-29 15:16:54
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû
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jiaoyixiong

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¡¾´ð°¸¡¿Ó¦Öú»ØÌû

¡ï ¡ï ¡ï ¡ï ¡ï
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zh1987hs: ½ð±Ò+5, лл 2012-08-28 08:42:51
Èç¹ûÄãÊÇÓÃNAMD×öÄ£Ä⣬ÄãʹÓÃÏÂÃæÕâ¶Î½Å±¾¾ÍÐÐ

package require psfgen
resetpsf
readpsf temp-1.psf
coordpdb temp-1.pdb
readpsf temp-2.psf
coordpdb temp-2.pdb
writepsf temp.psf
writepdb temp.pdb

¾ÍÐÐÁË
2Â¥2012-08-28 08:27:38
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

tanzouqing

гæ (СÓÐÃûÆø)

ÒýÓûØÌû:
2Â¥: Originally posted by jiaoyixiong at 2012-08-28 08:27:38
Èç¹ûÄãÊÇÓÃNAMD×öÄ£Ä⣬ÄãʹÓÃÏÂÃæÕâ¶Î½Å±¾¾ÍÐÐ

package require psfgen
resetpsf
readpsf temp-1.psf
coordpdb temp-1.pdb
readpsf temp-2.psf
coordpdb temp-2.pdb
writepsf temp.psf
writepdb temp.pd ...

±ØÐëÒªÓÐÏàÓ¦µÄpsfÎļþÂð?
×î³õµÄÄ¿µÄ:
Ô­Îļþtemp-1.pdbºÍtemp-1.psf,ÀïÃæ½öÒ»ÌõÁ´, ÎÒÏëµÃµ½Á½¸öÁ´,ÏÈmovebyÔ­ÓÐÁ´,±£´æÒƶ¯ºóµÄtemp-2.pdb,µ«²»ÖªÔõôµÃµ½Òƶ¯ºóµÄtemp-2.psf??
3Â¥2012-08-28 18:50:50
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

jiaoyixiong

ÈÙÓþ°æÖ÷ (Ö°Òµ×÷¼Ò)

¡¾´ð°¸¡¿Ó¦Öú»ØÌû

¡ï ¡ï ¡ï
zh1987hs: ½ð±Ò+3, лл 2012-08-28 20:28:57
ÒýÓûØÌû:
3Â¥: Originally posted by tanzouqing at 2012-08-28 18:50:50
±ØÐëÒªÓÐÏàÓ¦µÄpsfÎļþÂð?
×î³õµÄÄ¿µÄ:
Ô­Îļþtemp-1.pdbºÍtemp-1.psf,ÀïÃæ½öÒ»ÌõÁ´, ÎÒÏëµÃµ½Á½¸öÁ´,ÏÈmovebyÔ­ÓÐÁ´,±£´æÒƶ¯ºóµÄtemp-2.pdb,µ«²»ÖªÔõôµÃµ½Òƶ¯ºóµÄtemp-2.psf??...

ÄãÒÆ¶¯Ö®ºóµÃµ½temp-2.pdbÊÇͨ¹ý
writepdb temp-2.pdb °É£¿
ͬÑù¿ÉÒÔ
$sel writepsf temp-2.psf

¾ÍÐÐÁË£¬²»¹ýÐèÒªÐÞ¸ÄһϠtemp-2.pdb ºÍtemp-2.psf µÄsegname,
²»È»ÔÚʹÓÃÉÏÃæµÄ½Å±¾ºÏ²¢µÄʱºò»á±¨´í
4Â¥2012-08-28 19:56:55
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

tanzouqing

гæ (СÓÐÃûÆø)

ÒýÓûØÌû:
4Â¥: Originally posted by jiaoyixiong at 2012-08-28 19:56:55
ÄãÒÆ¶¯Ö®ºóµÃµ½temp-2.pdbÊÇͨ¹ý
writepdb temp-2.pdb °É£¿
ͬÑù¿ÉÒÔ
$sel writepsf temp-2.psf

¾ÍÐÐÁË£¬²»¹ýÐèÒªÐÞ¸ÄһϠtemp-2.pdb ºÍtemp-2.psf µÄsegname,
²»È»ÔÚʹÓÃÉÏÃæµÄ½Å±¾ºÏ²¢µÄʱºò»á±¨´í...

°æÖ÷,ÄúºÃ,ÈçºÎÐÞ¸Äsegname?
¹éÄÉϲ½Öè:
step 1.Éú³Étemp-2.dpbºÍtemp-2.psf
mol new temp-1.pdb;mol addfile temp-1.psf
set allsel [atomselect top all]
$allsel writepdb temp-2.pdb;$allsel wirtepsf temp-2.psf

step 2.ÐÞ¸Ä temp-2.pdb ºÍtemp-2.psf µÄsegname
Õâ²½²»ÖªÈçºÎÐÞ¸Ä?·³Çë°ïæ

step 3.ÎļþºÏ²¢
package require psfgen;resetpsf
readpsf temp-1.psf;coordpdb temp-1.pdb
readpsf temp-2.psf;coordpdb temp-2.pdb
writepsf temp.psf;writepdb temp.pd
5Â¥2012-08-29 11:21:42
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

jiaoyixiong

ÈÙÓþ°æÖ÷ (Ö°Òµ×÷¼Ò)

¡¾´ð°¸¡¿Ó¦Öú»ØÌû

¡ï ¡ï
zh1987hs: ½ð±Ò+2, лл 2012-08-29 14:47:19
ÒýÓûØÌû:
5Â¥: Originally posted by tanzouqing at 2012-08-29 11:21:42
°æÖ÷,ÄúºÃ,ÈçºÎÐÞ¸Äsegname?
¹éÄÉϲ½Öè:
step 1.Éú³Étemp-2.dpbºÍtemp-2.psf
mol new temp-1.pdb;mol addfile temp-1.psf
set allsel
$allsel writepdb temp-2.pdb;$allsel wirtepsf temp-2.psf

step 2 ...

Ö±½ÓÔÚµÚÒ»²½ÕâÀïÐ޸ļ´¿É

step 1.Éú³Étemp-2.dpbºÍtemp-2.psf
mol new temp-1.pdb;mol addfile temp-1.psf
set allsel [atomselect top all]
$allsel  set segname NEW
$allsel writepdb temp-2.pdb;$allsel wirtepsf temp-2.psf

¼´¿É
6Â¥2012-08-29 14:27:25
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

tanzouqing

гæ (СÓÐÃûÆø)

ÒýÓûØÌû:
6Â¥: Originally posted by jiaoyixiong at 2012-08-29 14:27:25
Ö±½ÓÔÚµÚÒ»²½ÕâÀïÐ޸ļ´¿É

step 1.Éú³Étemp-2.dpbºÍtemp-2.psf
mol new temp-1.pdb;mol addfile temp-1.psf
set allsel
$allsel  set segname NEW
$allsel writepdb temp-2.pdb;$allsel wirtepsf temp-2.p ...

ÒÔÉÏ·½·¨ÎÞ·¨µÃµ½ÕýÈ·µÄpsfÎļþ!!!
#´úÂëbegin
mol new temp-1.pdb ;mol addfile temp-1.psf
set allsel [atomselect top all]
$allsel moveby {0 0 10}
$allsel set segname new
$allsel writepdb temp-2.pdb ;$allsel writepsf temp-2.psf
#´úÂëend
½á¹û¶Ô±È:
temp-1.psfµÄ²¿·ÖÄÚÈÝ
    1904 !NATOM
       1 ADNA 1    ADE  H5T  HN5    0.430000        1.0080           0
       2 ADNA 1    ADE  O5'  ON5   -0.660000       15.9994           0
       3 ADNA 1    ADE  C5'  CN8    0.050000       12.0110           0
temp-2.psfµÄ²¿·ÖÄÚÈÝ,ÓëÇ°Ãæ²»´îÅä.     
     477 !NATOM
       1 new  2    DC   O5'  O5'    0.000000       15.9994           0
       2 new  2    DC   C5'  C5'    0.000000       12.0107           0
       3 new  2    DC   C4'  C4'    0.000000       12.0107           0
ÇÒºóÃæµÄ¼ü³¤,¼ü½Ç,¶þÃæ½Ç¶¼Îª0 .
7Â¥2012-08-29 15:00:26
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

tanzouqing

гæ (СÓÐÃûÆø)

ÒýÓûØÌû:
8Â¥: Originally posted by jiaoyixiong at 2012-08-29 15:16:54
Äã°Ñ¡°mol new temp-1.pdb ;mol addfile temp-1.psf¡±
¸Ä³É¡°mol load psf  temp-1.psf pdb temp-1.pdb¡±

»¹ÊDz»ÐÐ,ÎÞ·¨Òƶ¯...
>Main< (NAMD-work) 61 % $allsel moveby {0 0 10}
atomselection moveby: invalid/ no coordinates in selection
9Â¥2012-08-29 15:36:58
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

jiaoyixiong

ÈÙÓþ°æÖ÷ (Ö°Òµ×÷¼Ò)

ÒýÓûØÌû:
9Â¥: Originally posted by tanzouqing at 2012-08-29 15:36:58
»¹ÊDz»ÐÐ,ÎÞ·¨Òƶ¯...
>Main< (NAMD-work) 61 % $allsel moveby {0 0 10}
atomselection moveby: invalid/ no coordinates in selection...

°ÑÄãµÄtemp-1.psf ºÍtemp-1.pdbÌùÔÚ¸½¼þÀÎÒÊÔÊÔ

» ±¾ÌûÒÑ»ñµÃµÄºì»¨£¨×îÐÂ10¶ä£©

10Â¥2012-08-29 15:44:46
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû
Ïà¹Ø°æ¿éÌø×ª ÎÒÒª¶©ÔÄÂ¥Ö÷ tanzouqing µÄÖ÷Ìâ¸üÐÂ
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